1
|
Li L, Li C, Guo H, Liu Y, Sheng J, Guo S, Shen Q, Ling N, Guo J. Enhanced carbon use efficiency and warming resistance of soil microorganisms under organic amendment. ENVIRONMENT INTERNATIONAL 2024; 192:109043. [PMID: 39369561 DOI: 10.1016/j.envint.2024.109043] [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: 06/24/2024] [Revised: 08/30/2024] [Accepted: 09/29/2024] [Indexed: 10/08/2024]
Abstract
The frequency and intensity of extreme weather events, including rapid temperature fluctuations, are increasing because of climate change. Long-term fertilization practices have been observed to alter microbial physiology and community structure, thereby affecting soil carbon sequestration. However, the effects of warming on the carbon sequestration potential of soil microbes adapted to long-term fertilization remain poorly understood. In this study, we utilized 18O isotope labeling to assess microbial carbon use efficiency (CUE) and employed stable isotope probing (SIP) with 18O-H2O to identify growing taxa in response to temperature changes (5-35 °C). Organic amendment with manure or straw residue significantly increased microbial CUE by 86-181 % compared to unfertilized soils. The microorganisms inhabiting organic amended soils displayed greater resistance of microbial CUE to high temperatures (25-35 °C) compared to those inhabiting soils fertilized only with minerals. Microbial growth patterns determined by the classification of taxa into incorporators or non-incorporators based on 18O incorporation into DNA exhibited limited phylogenetic conservation in response to temperature changes. Microbial clusters were identified by grouping taxa with similar growth patterns across different temperatures. Organic amendments enriched microbial clusters associated with increased CUE, whereas clusters in unfertilized or mineral-only fertilized soils were linked to decreased CUE. Specifically, shifts in the composition of growing bacteria were correlated with enhanced microbial CUE, whereas modifications in the composition of growing fungi were associated with diminished CUE. Notably, the responses of microbial CUE to temperature fluctuations were primarily driven by changes in the bacterial composition. Overall, our findings demonstrate that organic amendments enhance soil microbial CUE and promote the enrichment of specific microbial clusters that are better equipped to cope with temperature changes. This study establishes a theoretical foundation for manipulating soil microbes to enhance carbon sequestration under global climate scenarios.
Collapse
Affiliation(s)
- Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; Center for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu, China
| | - Chenhua Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China
| | - Hanyue Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunhua Liu
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China
| | - Jiandong Sheng
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, Xinjiang 830052, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; Center for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu, China
| | - Junjie Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Agriculture and Biotechnology, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
| |
Collapse
|
2
|
Serwecińska L, Font-Nájera A, Strapagiel D, Lach J, Tołoczko W, Bołdak M, Urbaniak M. Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils. Sci Rep 2024; 14:21034. [PMID: 39251745 PMCID: PMC11385149 DOI: 10.1038/s41598-024-71656-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 08/29/2024] [Indexed: 09/11/2024] Open
Abstract
Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable.
Collapse
Affiliation(s)
- Liliana Serwecińska
- European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Tylna 3, 90‑364, Lodz, Poland.
| | - Arnoldo Font-Nájera
- European Regional Centre for Ecohydrology of the Polish Academy of Sciences, Tylna 3, 90‑364, Lodz, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 139, 90-235, Lodz, Poland
| | - Jakub Lach
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 139, 90-235, Lodz, Poland
| | - Wojciech Tołoczko
- Department of Physical Geography, Faculty of Geographical Sciences, University of Lodz, Narutowicza 88, 90-139, Lodz, Poland
| | - Małgorzata Bołdak
- Department of Agriculture and Environmental Chemistry, University of Agriculture in Krakow, Mickiewicza 21, 31-120, Kraków, Poland
| | - Magdalena Urbaniak
- UNESCO Chair on Ecohydrology and Applied Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90‑237, Lodz, Poland
| |
Collapse
|
3
|
Pan H, Wattiez R, Gillan D. Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges. Curr Microbiol 2024; 81:257. [PMID: 38955825 DOI: 10.1007/s00284-024-03781-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.
Collapse
Affiliation(s)
- Haixia Pan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology (Panjin Campus), Panjin, China.
- Proteomics and Microbiology Department, University of Mons, Avenue du champ de Mars 6, 7000, Mons, Belgium.
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, Avenue du champ de Mars 6, 7000, Mons, Belgium
| | - David Gillan
- Proteomics and Microbiology Department, University of Mons, Avenue du champ de Mars 6, 7000, Mons, Belgium
| |
Collapse
|
4
|
Lei X, Cui G, Sun H, Hou S, Deng H, Li B, Yang Z, Xu Q, Huo X, Cai J. How do earthworms affect the pathway of sludge bio-stabilization via vermicomposting? THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170411. [PMID: 38280597 DOI: 10.1016/j.scitotenv.2024.170411] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 01/29/2024]
Abstract
The synergy effects between earthworms and microorganisms promote nitrogen mineralization and enhance stabilization of organic matters in a vermicomposting system. However, the stabilization pathways of vermicomposting in the system remain unknown. The aim of this study was to investigate the effect of earthworms on the stabilization pathway and associated microbial population of waste activated sludge recycled by vermicomposting. The treatment of sludge with and without earthworms was conducted at 20 °C for 60 days. The trends in organic matter (OM), dissolved organic carbon (DOC), NH4+-N, electrical conductivity (EC), microbial biomass carbon (MBC), and dehydrogenase activity (DHA) were similar in both systems over time. At the end of the treatment, OM and DOC were significantly lower (p < 0.05), and EC, NH4+-N, and NO3--N were significantly higher (p < 0.05) in the vermicomposting group than in the control. Based on the statistical results of principal component analysis (PCA), it was proposed that the stabilization pathway in both treatment systems required a sequence of reactions characterized by the degradation of organic matter, accumulation of dissolved organic carbon, ammonification, and nitrification. Vermicomposting led to greater abundance and diversity (Shannon index) of 16S rDNA microbial species, but more even distribution in microbial community composition (Simpson index) than the control. However, the opposite performance for 18S rDNA microbes was observed. Vermicomposting enhanced the abundance of microorganisms involved in organic matter degradation and nitrification, facilitating the conversion of organic matter and favoring the nitrification. In short, the pathway of sludge bio-stabilization is not altered regardless of the addition of earthworms or not, which enables us to better understand vermicomposting process of sludge.
Collapse
Affiliation(s)
- Xuyang Lei
- Department of Resource and Environmental Engineering, Hebei Vocational University of Technology and Engineering, Hebei, Xingtai 054000, China
| | - Guangyu Cui
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Hongxin Sun
- Department of Resource and Environmental Engineering, Hebei Vocational University of Technology and Engineering, Hebei, Xingtai 054000, China
| | - Suxia Hou
- Department of Resource and Environmental Engineering, Hebei Vocational University of Technology and Engineering, Hebei, Xingtai 054000, China
| | - Hongying Deng
- Department of Resource and Environmental Engineering, Hebei Vocational University of Technology and Engineering, Hebei, Xingtai 054000, China
| | - Bo Li
- Department of Resource and Environmental Engineering, Hebei Vocational University of Technology and Engineering, Hebei, Xingtai 054000, China
| | - Zhengzheng Yang
- Department of Resource and Environmental Engineering, Hebei Vocational University of Technology and Engineering, Hebei, Xingtai 054000, China
| | - Qiushi Xu
- Department of Resource and Environmental Engineering, Hebei Vocational University of Technology and Engineering, Hebei, Xingtai 054000, China
| | - Xueyu Huo
- Department of Resource and Environmental Engineering, Hebei Vocational University of Technology and Engineering, Hebei, Xingtai 054000, China
| | - Jiaxuan Cai
- Department of Resource and Environmental Engineering, Hebei Vocational University of Technology and Engineering, Hebei, Xingtai 054000, China
| |
Collapse
|
5
|
Mula-Michel H, White P, Hale A. Immediate impacts of soybean cover crop on bacterial community composition and diversity in soil under long-term Saccharum monoculture. PeerJ 2023; 11:e15754. [PMID: 37637164 PMCID: PMC10452624 DOI: 10.7717/peerj.15754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/26/2023] [Indexed: 08/29/2023] Open
Abstract
Saccharum yield decline results from long-term monoculture practices. Changes in cropping management can improve soil health and productivity. Below-ground bacterial community diversity and composition across soybean (Glycine max (L.) Merr) cover crop, Saccharum monoculture (30+ year) and fallowed soil were determined. Near full length (~1,400 base pairs) of 16S rRNA gene sequences were extracted from the rhizospheres of sugarcane and soybean and fallowed soil were compared. Higher soil bacterial diversity was observed in the soybean cover crop than sugarcane monoculture across all measured indices (observed operationational taxonomic units, Chao1, Shannon, reciprocal Simpson and Jackknife). Acidocateria, Proteobacteria, Bacteroidetes and Planctomycetes were the most abundant bacterial phyla across the treatments. Indicator species analysis identified nine indicator phyla. Planctomycetes, Armatimonadetes and candidate phylum FBP were associated with soybean; Proteobacteria and Firmicutes were linked with sugarcane and Gemmatimonadetes, Nitrospirae, Rokubacteria and unclassified bacteria were associated with fallowed soil. Non-metric multidimensional scaling analysis showed distinct groupings of bacterial operational taxonomic units (97% identity) according to management system (soybean, sugarcane or fallow) indicating compositional differences among treatments. This is confirmed by the results of the multi-response permutation procedures (A = 0.541, p = 0.00045716). No correlation between soil parameters and bacterial community structure was observed according to Mantel test (r = 211865, p = 0.14). Use of soybean cover-crop fostered bacterial diversity and altered community structure. This indicates cover crops could have a restorative effect and potentially promote sustainability in long-term Saccharum production systems.
Collapse
Affiliation(s)
- Himaya Mula-Michel
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, USDA-ARS, Sugarcane Research Unit, Houma, LA, USA
| | - Paul White
- USDA-ARS, Sugarcane Research Unit, Houma, LA, USA
| | - Anna Hale
- USDA-ARS, Sugarcane Research Unit, Houma, LA, USA
| |
Collapse
|
6
|
Cui Y, Peng S, Delgado-Baquerizo M, Rillig MC, Terrer C, Zhu B, Jing X, Chen J, Li J, Feng J, He Y, Fang L, Moorhead DL, Sinsabaugh RL, Peñuelas J. Microbial communities in terrestrial surface soils are not widely limited by carbon. GLOBAL CHANGE BIOLOGY 2023; 29:4412-4429. [PMID: 37277945 DOI: 10.1111/gcb.16765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/07/2023]
Abstract
Microbial communities in soils are generally considered to be limited by carbon (C), which could be a crucial control for basic soil functions and responses of microbial heterotrophic metabolism to climate change. However, global soil microbial C limitation (MCL) has rarely been estimated and is poorly understood. Here, we predicted MCL, defined as limited availability of substrate C relative to nitrogen and/or phosphorus to meet microbial metabolic requirements, based on the thresholds of extracellular enzyme activity across 847 sites (2476 observations) representing global natural ecosystems. Results showed that only about 22% of global sites in terrestrial surface soils show relative C limitation in microbial community. This finding challenges the conventional hypothesis of ubiquitous C limitation for soil microbial metabolism. The limited geographic extent of C limitation in our study was mainly attributed to plant litter, rather than soil organic matter that has been processed by microbes, serving as the dominant C source for microbial acquisition. We also identified a significant latitudinal pattern of predicted MCL with larger C limitation at mid- to high latitudes, whereas this limitation was generally absent in the tropics. Moreover, MCL significantly constrained the rates of soil heterotrophic respiration, suggesting a potentially larger relative increase in respiration at mid- to high latitudes than low latitudes, if climate change increases primary productivity that alleviates MCL at higher latitudes. Our study provides the first global estimates of MCL, advancing our understanding of terrestrial C cycling and microbial metabolic feedback under global climate change.
Collapse
Affiliation(s)
- Yongxing Cui
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Shushi Peng
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | | | - César Terrer
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Boston, Massachusetts, USA
| | - Biao Zhu
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Xin Jing
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ji Chen
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Jinquan Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiao Feng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yue He
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Linchuan Fang
- School of Resource and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - Daryl L Moorhead
- Department of Environmental Sciences, University of Toledo, Toledo, Ohio, USA
| | - Robert L Sinsabaugh
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, Catalonia, Spain
| |
Collapse
|
7
|
Li Z, Wang J, Wu Y, Hu J, Cong L, Yang C, Fu J, Sun J. Changes in soil properties and the phoD-harboring bacteria of the alfalfa field in response to phosphite treatment. Front Microbiol 2022; 13:1013896. [DOI: 10.3389/fmicb.2022.1013896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/02/2022] [Indexed: 11/30/2022] Open
Abstract
Phosphite, a reduced form of orthophosphate, is characterized by high solubility, and transportation efficiency and can be used as potential phosphorus fertilizer, plant biostimulant and supplemental fertilizer in agriculture. However, the effects of phosphite fertilizer on soil properties and microorganisms are poorly understood. This study evaluated the effects of phosphate and phosphite fertilizers on the different forms of phosphorus, alkaline phosphatase (ALP) activity, and phoD-harboring bacterial community in the alfalfa (Medicago sativa) field. The study used four concentrations (30, 60, 90, and 120 mg P2O5 kg−1 soil) of phosphate (KH2PO4) and phosphite (KH2PO3) fertilizers for the alfalfa field treatment. The results showed that both phosphite and phosphate fertilizers increased the total phosphorus (TP) and available phosphorus (AP) contents in the soil. The phosphorus content of the phosphite-treated soil was lower than that of the phosphate-treated one. TP, inorganic phosphate (Pi), and AP negatively regulated ALP activity, which decreased with increasing phosphate and phosphite fertilizers concentrations. Furthermore, high-throughput sequencing analysis identified 6 phyla and 29 families, which were classified from the altered operational taxonomic units (OTUs) of the soil samples. The redundancy analysis (RDA) revealed that pH, TP, AP and Pi were significantly related to the phoD-harboring bacterial community constructure. The different fertilizer treatments altered the key families, contributing to soil ALP activities. Frankiaceae, Sphingomonadaceae, and Rhizobiaceae positively correlated with ALP activity in phosphite-treated soil. Moreover, the structural equation model (SEM) revealed that ALP activity was affected by the phoD-harboring bacterial community through altered organic phosphorus (Po), AP, total nitrogen (TN), soil organic carbon (SOC), and pH levels under phosphate fertilizer treatment. However, the effect was achieved through positive regulation of pH and AP under phosphite fertilizer. Thus, the changes in soil properties and phoD-harboring bacteria in response to phosphate and phosphite treatments differed in the alfalfa field. This study is the first to report the effects of phosphite on the soil properties of an alfalfa field and provides a strong basis for phosphite utilization in the future.Highlights– Phosphite and phosphate increase the total phosphorus and available phosphorus.– The pH was the dominant factor influencing the phoD-harboring bacterial community under phosphite fertilizer.– The response of soil properties and phoD-harboring bacterial community to phosphate and phosphite fertilizers differed in the alfalfa field.
Collapse
|
8
|
Qiao X, Sun T, Lei J, Xiao L, Xue L, Zhang H, Jia J, Bei S. Arbuscular mycorrhizal fungi contribute to wheat yield in an agroforestry system with different tree ages. Front Microbiol 2022; 13:1024128. [DOI: 10.3389/fmicb.2022.1024128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
Intercropping achieved through agroforestry is increasingly being recognized as a sustainable form of land use. In agroforestry, the roots of trees and crops are intermingled, and their interactions and the production of exudates alter the soil environment and soil microbial community. Although tree–crop interactions vary depending on the stand age of the trees, how stand age affects beneficial microorganisms, including arbuscular mycorrhizal fungi (AMF), and whether changes in soil microorganisms feed back on crop growth in agroforestry systems are unknown. We therefore conducted a long-term field study to compare changes in the soil microbial and AMF communities in a jujube/wheat agroforestry system containing trees of different stand ages: 3-year-old jujube, 8-year-old jujube, and 13-year-old jujube. Our results showed that by changing soil moisture and available phosphorus content, the stand age of the trees had a significant effect on the soil microbial and AMF communities. Soil moisture altered the composition of soil bacteria, in particular the proportions of Gram-positive and Gram-negative species, and available phosphorus had significant effects on the AMF community. A network analysis showed that older stands of trees reduced both AMF diversity and network complexity. An ordinary least squares regression analysis indicated that AMF diversity, network complexity, and stability contributed to wheat yield. Finally, structural equation modeling showed that changes in edaphic factors induced by tree age brought about significant variation in the soil microbial and AMF communities, in turn, affecting crop growth. Our study highlights the crucial roles of soil microorganisms, in particular AMF, in supporting plant growth in agroforestry systems as well as the need to consider stand age in the establishment of these systems.
Collapse
|
9
|
Yang J, Masoudi A, Li H, Gu Y, Wang C, Wang M, Yu Z, Liu J. Microbial community structure and niche differentiation under different health statuses of Pinus bungeana in the Xiong'an New Area in China. Front Microbiol 2022; 13:913349. [PMID: 36118200 PMCID: PMC9481298 DOI: 10.3389/fmicb.2022.913349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Pinus bungeana is a native but endangered plant species in China, with high ornamental value and adaptability to drought and cold. The relationship between the soil community structure and endophytic microbes in the tissues of P. bungeana under different health statuses is poorly understood. In this study, the endophytic bacterial and fungal communities of P. bungeana under different health statuses were compared and analyzed in the Xiong'an New Area. Using high-throughput deep sequencing [16S and internal transcribed spacer (ITS) rRNA] techniques, the effect of the health status of P. bungeana on the microbial communities in bulk soil, rhizospheric soil, roots, stems, and leaves was determined in this study. We observed that the diversity of the bacterial and fungal communities of the aboveground parts (stems and leaves) of healthy P. bungeana plants was much higher than that of the unhealthy plants. However, the diversity of bacterial and fungal communities in the belowground parts (bulk soil, rhizospheric soil, and roots) showed almost no difference in microbial community richness, indicating that the possible cause of illness was transmitted in a "top-down" manner. Furthermore, there were significant differences in the microbial diversity and community structure in different ecological niches of P. bungeana (P < 0.01). Proteobacteria and Actinobacteria were the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the predominant fungal phyla. Redundancy analysis (RDA) revealed that soil organic matter (SOM), total phosphorous (TP), total potassium (TK), total nitrogen (TN), water content (WC), power of hydrogen (pH), total carbon (TC), and the ratio of carbon to nitrogen (C/N) were significantly correlated with the composition of the microbial communities. Altogether, these results provide a scientific basis for further studies on the mechanism underlying the "aboveground-underground" microbial interactions in plantation forests, which can aid in promoting the healthy and sustainable development of the Millennium Xiulin forest in the Xiong'an New Area.
Collapse
Affiliation(s)
- Jia Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Abolfazl Masoudi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Hao Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yifan Gu
- School of Geographic Sciences, Hebei Normal University, Shijiazhuang, China
| | - Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| |
Collapse
|
10
|
Wang M, Wu Y, Zhao J, Liu Y, Chen Z, Tang Z, Tian W, Xi Y, Zhang J. Long-term fertilization lowers the alkaline phosphatase activity by impacting the phoD-harboring bacterial community in rice-winter wheat rotation system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153406. [PMID: 35092777 DOI: 10.1016/j.scitotenv.2022.153406] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/16/2022] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
PhoD-harboring bacteria and the secreted alkaline phosphatases (ALP) are crucial in the regulation of soil phosphorus (P) cycling. However, the influential factors of these crucial indicators and their internal interactions remain controversial. Here, a long-term field experiment containing different fertilization regimes was conducted (chemical, organic, and no fertilizer applied). The results indicated that the richness and diversity of phoD-harboring bacterial community were significantly decreased after long-term fertilization. The applied fertilizer promoted the growth of competitive species, while phoD-harboring bacteria lost the advantage to outcompete other microorganisms after long-term fertilization. The decreased ALP activity was caused by the declined phoD gene abundance, which is attributed to the comprehensive effects of soil organic C (SOC), total nitrogen (TN), and various forms of P. The random forest models identified SOC, TN, and available P (AP) to be the dominant environmental factors in shaping the phoD-harboring bacterial community. In addition, some other forms of P such as organic P (Po), inorganic P (Pi) or total P (TP) also exerted significant effects. Different fertilization regimes changed the keystone genera that contributed significantly to soil ALP activities, while Pseudolabrys and Pseudomonas were predicted to be the most important genera regardless of different fertilization regimes. This study extends the understanding of the main process and mechanisms of P mobilization in response to different fertilization regimes.
Collapse
Affiliation(s)
- Mengmeng Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Yuncheng Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Jiayin Zhao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Yu Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Zhe Chen
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Zhaoyang Tang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Wei Tian
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China.
| | - Yunguan Xi
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Jibing Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| |
Collapse
|
11
|
Duan N, Li L, Liang X, Fine A, Zhuang J, Radosevich M, Schaeffer SM. Variation in Bacterial Community Structure Under Long-Term Fertilization, Tillage, and Cover Cropping in Continuous Cotton Production. Front Microbiol 2022; 13:847005. [PMID: 35444635 PMCID: PMC9015707 DOI: 10.3389/fmicb.2022.847005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Agricultural practices alter the structure and functions of soil microbial community. However, few studies have documented the alterations of bacterial communities in soils under long-term conservation management practices for continuous crop production. In this study, we evaluated soil bacterial diversity using 16S rRNA gene sequencing and soil physical and chemical properties within 12 combinations of inorganic N fertilization, cover cropping, and tillage throughout a cotton production cycle. Soil was collected from field plots of the West Tennessee Agriculture Research and Education Center in Jackson, TN, United States. The site has been under continuous cotton production for 38 years. A total of 38,038 OTUs were detected across 171 soil samples. The dominant bacterial phyla were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, accounting for ∼70% of the total bacterial community membership. Conventional tillage increased alpha diversity in soil samples collected in different stages of cotton production. The effects of inorganic N fertilization and conventional tillage on the structure of bacterial communities were significant at all four sampling dates (p < 0.01). However, cover cropping (p < 0.05) and soil moisture content (p < 0.05) only showed significant influence on the bacterial community structure after burn-down of the cover crops and before planting of cotton (May). Nitrate-N appeared to have a significant effect on the structure of bacterial communities after inorganic fertilization and at the peak of cotton growth (p < 0.01). Structural equation modeling revealed that the relative abundances of denitrifying and nitrifying bacteria were higher when conventional tillage and vetch cover crop practices were applied, respectively. Our results indicate that long-term tillage and fertilization are key factors increasing the diversity and restructuring the composition of bacterial communities, whereas cover cropping may have shorter-term effects on soil bacteria community structure. In this study, management practices might positively influence relative abundances of bacterial functional groups associated with N cycling. The bacteria functional groups may build a network for providing N and meet microbial N needs in the long term.
Collapse
Affiliation(s)
- Ning Duan
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Lidong Li
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Xiaolong Liang
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Aubrey Fine
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Jie Zhuang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sean M. Schaeffer
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, United States
| |
Collapse
|
12
|
Rawat VS, Kaur J, Bhagwat S, Pandit MA, Rawat CD. Deploying Microbes as Drivers and Indicators in Ecological Restoration. Restor Ecol 2022. [DOI: 10.1111/rec.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Jasleen Kaur
- Department of Botany, Dyal Singh College University of Delhi New Delhi 110003 India
| | - Sakshi Bhagwat
- Department of Biosciences Faculty of Natural Sciences, Jamia Millia Islamia New Delhi 110025 India
| | - Manisha Arora Pandit
- Department of Zoology, Kalindi College University of Delhi New Delhi 110008 India
| | - Charu Dogra Rawat
- Molecular Biology and Genomics Research Laboratory, Ramjas College University of Delhi Delhi 110007 India
- Department of Zoology, Ramjas College University of Delhi Delhi 110007 India
| |
Collapse
|
13
|
Mondini A, Anwar MZ, Ellegaard-Jensen L, Lavin P, Jacobsen CS, Purcarea C. Heat Shock Response of the Active Microbiome From Perennial Cave Ice. Front Microbiol 2022; 12:809076. [PMID: 35360653 PMCID: PMC8960993 DOI: 10.3389/fmicb.2021.809076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/28/2021] [Indexed: 11/13/2022] Open
Abstract
Ice caves constitute the newly investigated frozen and secluded model habitats for evaluating the resilience of ice-entrapped microbiomes in response to climate changes. This survey identified the total and active prokaryotic and eukaryotic communities from millennium-old ice accumulated in Scarisoara cave (Romania) using Illumina shotgun sequencing of the ribosomal RNA (rRNA) and messenger RNA (mRNA)-based functional analysis of the metatranscriptome. Also, the response of active microbiome to heat shock treatment mimicking the environmental shift during ice melting was evaluated at both the taxonomic and metabolic levels. The putatively active microbial community was dominated by bacterial taxa belonging to Proteobacteria and Bacteroidetes, which are highly resilient to thermal variations, while the scarcely present archaea belonging to Methanomicrobia was majorly affected by heat shock. Among eukaryotes, the fungal rRNA community was shared between the resilient Chytridiomycota and Blastocladiomycota, and the more sensitive Ascomycota and Basidiomycota taxa. A complex microeukaryotic community highly represented by Tardigrada and Rotifera (Metazoa), Ciliophora and Cercozoa (Protozoa), and Chlorophyta (Plantae) was evidenced for the first time in this habitat. This community showed a quick reaction to heat shock, followed by a partial recovery after prolonged incubation at 4°C due to possible predation processes on the prokaryotic cluster. Analysis of mRNA differential gene expression revealed the presence of an active microbiome in the perennial ice from the Scarisoara cave and associated molecular mechanisms for coping with temperature variations by the upregulation of genes involved in enzyme recovery, energy storage, carbon and nitrogen regulation, and cell motility. This first report on the active microbiome embedded in perennial ice from caves and its response to temperature stress provided a glimpse into the impact of glaciers melting and the resilience mechanisms in this habitat, contributing to the knowledge on the functional role of active microbes in frozen environments and their response to climatic changes.
Collapse
Affiliation(s)
- Antonio Mondini
- Department of Microbiology, Institute of Biology, Bucharest, Romania
| | - Muhammad Zohaib Anwar
- Department of Environmental Science, Aarhus University, RISØ Campus, Roskilde, Denmark
- Center for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Lea Ellegaard-Jensen
- Department of Environmental Science, Aarhus University, RISØ Campus, Roskilde, Denmark
| | - Paris Lavin
- Centre of Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Carsten Suhr Jacobsen
- Department of Environmental Science, Aarhus University, RISØ Campus, Roskilde, Denmark
| | - Cristina Purcarea
- Department of Microbiology, Institute of Biology, Bucharest, Romania
- *Correspondence: Cristina Purcarea,
| |
Collapse
|
14
|
Steponavičienė V, Bogužas V, Sinkevičienė A, Skinulienė L, Vaisvalavičius R, Sinkevičius A. Soil Water Capacity, Pore Size Distribution, and CO 2 Emission in Different Soil Tillage Systems and Straw Retention. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050614. [PMID: 35270083 PMCID: PMC8912575 DOI: 10.3390/plants11050614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 05/26/2023]
Abstract
The long-term implementation of crop rotation and tillage has an impact on the soil environment through inputs and soil disturbance, which in turn has an impact on soil quality. Tillage has a long-term impact on the agroecosystems. Since 1999, a long-term field experiment has been carried out at the Experimental Station of Vytautas Magnus University. The aim of this experiment is to investigate the effects of long-term various-intensity tillage and straw retention systems on soil physical properties. The results were obtained in 2013 and 2019 (spring rape was growing). According to the latest edition of the International Soil Classification System, the soil in the experimental field was classified as Endocalcaric Stagnosol (Aric, Drainic, Ruptic, and Amphisiltic). The treatments were arranged using a split-plot design. In a two-factor field experiment, the straw was removed from one part of the experimental field, and the entire straw yield was chopped and spread at harvest in the other part of the field (Factor A). There were three different tillage systems as a subplot (conventional deep ploughing, cover cropping with following shallow termination, and no-tillage) (Factor B). There were four replications. The long-term application of reduced tillage significantly increased soil water retention and improved the pore structure and CO2 emissions. Irrespective of the incorporation of straw, it was found that as the amount of water available to plants increases, CO2 emissions from the soil increase to some extent and then start to decrease. Simplified tillage and no-tillage in uncultivated soil reduce CO2 emissions by increasing the amount of water available to plants from 0.151 to 0.233 m3·m-3.
Collapse
|
15
|
Risueño Y, Petri C, Conesa HM. A critical assessment on the short-term response of microbial relative composition in a mine tailings soil amended with biochar and manure compost. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126080. [PMID: 33992925 DOI: 10.1016/j.jhazmat.2021.126080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/19/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Phytomanagement of tailings requires the use of soil conditioners to favour plant establishment, but their benefits on soil microbial composition need to be assessed. The goal of this work was to evaluate the effect of two organic amendments, manure compost and biochar, on soil bacterial and fungal composition at metallic mine tailings. The addition of compost caused stronger effects in most of soil parameters and microbial composition than biochar, especially at the initial stage of the experiment. However, the higher dependence on labile organic carbon for some bacterial groups at the treatments containing compost determined their decay along time (Flavobacteriales, Sphingobacteriales) and the appearance of other taxa more dependent on recalcitrant organic matter (Xanthomonadales, Myxococcales). Biochar favoured bacterial decomposers (Actinomycetales) specialised in high lignin and other recalcitrant carbon compounds. Unlike bacteria, only a few fungal orders increased their relative abundances in the treatments containing compost (Sordariales and Microascales) while the rest showed a decrease or remained unaltered. The mix biochar-compost may result the best option to support a more diverse microbial population in terms of soil functionality that is able to decompose both labile and recalcitrant carbon compounds. This may favour the resilience of the system against environmental stressors.
Collapse
Affiliation(s)
- Yolanda Risueño
- Universidad Politécnica de Cartagena, Escuela Técnica Superior de Ingeniería Agronómica, Departamento de Ingeniería Agronómica, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain.
| | - César Petri
- IHSM-UMA-CSIC La Mayora, Departamento de Fruticultura Subtropical y Mediterránea, Avenida Dr. Wienberg, s/n, 29750 Algarrobo-Costa, Málaga, Spain.
| | - Héctor M Conesa
- Universidad Politécnica de Cartagena, Escuela Técnica Superior de Ingeniería Agronómica, Departamento de Ingeniería Agronómica, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain.
| |
Collapse
|
16
|
Abstract
Opencast mining drastically alters the landscape due to complete vegetation suppression and removal of topsoil layers. Precise indicators able to address incremental changes in soil quality are necessary to monitor and evaluate mineland rehabilitation projects. For this purpose, metaproteomics may be a useful tool due to its capacity to shed light on both taxonomic and functional overviews of soil biodiversity, allowing the linkage between proteins found in soil and ecosystem functioning. We investigated bacterial proteins and peptide abundance of three different mineland rehabilitation stages and compared it with a non-rehabilitated site and a native area (evergreen dense forest) in the eastern Amazon. The total amount of identified soil proteins was significantly higher in the rehabilitating and native soils than in the non-rehabilitated site. Regarding soil bacterial composition, the intermediate and advanced sites were shown to be most similar to native soil. Cyanobacteria and Firmicutes phyla are abundant in the early stages of environmental rehabilitation, while Proteobacteria population dominates the later stages. Enzyme abundances and function in the three rehabilitation stages were more similar to those found in the native soil, and the higher accumulation of many hydrolases and oxidoreductases reflects the improvement of soil biological activity in the rehabilitating sites when compared to the non-rehabilitated areas. Moreover, critical ecological processes, such as carbon and nitrogen cycling, seem to return to the soil in short periods after the start of rehabilitation activities (i.e., 4 years). Metaproteomics revealed that the biochemical processes that occur belowground can be followed throughout rehabilitation stages, and the enzymes shown here can be used as targets for environmental monitoring of mineland rehabilitation projects.
Collapse
|
17
|
He L, Ren Y, Zeng W, Wu X, Shen L, Yu R, Liu Y, Li J. Deciphering the Endophytic and Rhizospheric Microbial Communities of a Metallophyte Commelina communis in Different Cu-Polluted Soils. Microorganisms 2021; 9:microorganisms9081689. [PMID: 34442769 PMCID: PMC8399850 DOI: 10.3390/microorganisms9081689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/29/2021] [Accepted: 08/04/2021] [Indexed: 11/24/2022] Open
Abstract
Metallophytes microbiota play a key role in plant growth and resistance to heavy metal stress. Comparing to the well-studied single or some specific plant growth-promoting (PGP) bacterial strains, our current understanding of the structural and functional variations of microbiome of metallophytes is still limited. Here, we systematically investigated the endophytic and rhizosphere bacterial community profiles of a metallophyte Commelina communis growing in different Cu-polluted soils by high-throughput sequencing technology. The results showed that the rhizosphere communities of C. communis exhibited a much higher level of diversity and richness than the endosphere communities. Meanwhile, shifts in the bacterial community composition were observed between the rhizosphere and endosphere of C. communis, indicating plant compartment was a strong driver for the divergence between rhizosphere and endosphere community. Among the environmental factors, soil Cu content, followed by OM, TP and TN, played major roles in shaping the bacterial community structure of C. communis. At the highly Cu-contaminated site, Pseudomonas and Sphingomonas were the predominant genera in the endophytic and rhizospheric bacterial communities, respectively, which might enhance copper tolerance as PGP bacteria. In summary, our findings will be useful to better understand metallophyte–microbe interactions and select suitable bacterial taxa when facilitating phytoremediation.
Collapse
Affiliation(s)
- Li He
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (L.H.); (Y.R.); (W.Z.); (X.W.); (L.S.); (R.Y.); (Y.L.)
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University (CSU), Changsha 410083, China
| | - Yanzhen Ren
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (L.H.); (Y.R.); (W.Z.); (X.W.); (L.S.); (R.Y.); (Y.L.)
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University (CSU), Changsha 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (L.H.); (Y.R.); (W.Z.); (X.W.); (L.S.); (R.Y.); (Y.L.)
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University (CSU), Changsha 410083, China
| | - Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (L.H.); (Y.R.); (W.Z.); (X.W.); (L.S.); (R.Y.); (Y.L.)
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University (CSU), Changsha 410083, China
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (L.H.); (Y.R.); (W.Z.); (X.W.); (L.S.); (R.Y.); (Y.L.)
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University (CSU), Changsha 410083, China
| | - Runlan Yu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (L.H.); (Y.R.); (W.Z.); (X.W.); (L.S.); (R.Y.); (Y.L.)
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University (CSU), Changsha 410083, China
| | - Yuandong Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (L.H.); (Y.R.); (W.Z.); (X.W.); (L.S.); (R.Y.); (Y.L.)
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University (CSU), Changsha 410083, China
| | - Jiaokun Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; (L.H.); (Y.R.); (W.Z.); (X.W.); (L.S.); (R.Y.); (Y.L.)
- Correspondence:
| |
Collapse
|
18
|
A Narrative Review of the Facts and Perspectives on Agricultural Fertilization in Europe, with a Focus on Italy. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7060158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Fertilizers stand at the base of current agricultural practices, providing the nutrient sustainment required for growing plants. Most fertilizers are synthetic chemicals, whose exploitation at very high levels poses a risk to cultivated land and the whole environment. They have several drawbacks including soil degradation, water pollution, and human food safety. Currently, the urgent need to counterbalance these negative environmental impacts has opened the way for the use of natural and renewable products that may help to restore soil structure, microorganism communities, nutrient elements, and, in some cases, to positively enhance carbon soil sequestration. Here, we endeavor to reinforce the vision that effective strategies designed to mitigate negative anthropic and climate change impacts should combine, in appropriate proportions, solutions addressed to a lower and less energy intensive production of chemicals and to a more inclusive exploitation of renewable natural products as biological soil amendments. After drawing an overview of the agricultural energy demand and consumption of fertilizers in Europe in the last few years (with a particular focus on Italy), this narrative review will deal with the current and prospective use of compost, biochar, and neem cake, which are suitable natural products with well-known potential and still-to-be-discovered features, to benefit sustainable agriculture and be adopted as circular economic solutions.
Collapse
|
19
|
Rodríguez-Berbel N, Soria R, Ortega R, Bastida F, Miralles I. Quarry restoration treatments from recycled waste modify the physicochemical soil properties, composition and activity of bacterial communities and priming effect in semi-arid areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 774:145693. [PMID: 33607438 DOI: 10.1016/j.scitotenv.2021.145693] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
The selection of a suitable organic amendment for recovery of semi-arid soils degraded by mining is key to the success of an ecological restoration. The aim of this research is to study the short-term responses of physicochemical, biochemical and biological properties, as well as the changes of a soil bacterial community at the genus level after application of five types of organic amendments in a limestone quarry in Almería (SE, Spain). The relationship among bacterial taxa with biochemical and physicochemical properties and priming effect from restored soils was also analysed. Six months after the application of organic amendments, the values of different soil status, such as total organic carbon, total nitrogen, assimilable phosphorus and labile organic matter forms (carbohydrates and polyphenols), basal respiration (BR) and enzymatic activities increased significantly with respect to unrestored soils. Similarly, a positive priming effect of soil organic matter mineralisation was produced by all organic amendments, being significantly higher (p < 0.05) in sewage sludge-treated soils. Bacterial diversity was higher in restored than in control soils. The restoration caused changes in soil bacterial communities' composition at the phylum and genus levels. It was observed that soil bacterial communities were significantly related to several physical, chemical and biochemical soil properties, establishing two different co-occurrence patterns between restored and unrestored soils. A first bacterial co-occurrence pattern showed significant positive correlations to pH and C/N ratio and negativity with the rest of the soil properties. The second bacterial pattern was positively correlated with carbohydrates, μg of C, priming effect, BR, β-glucosidase and phosphatase and negatively with pH and C/N ratio. It was concluded that soil bacterial communities are clearly influenced by the types of organic amendments applied. Bacterial taxa such as Taibaiella or Pseudomonas could perform key functions in the carbon cycle in restored soils.
Collapse
Affiliation(s)
- N Rodríguez-Berbel
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain
| | - R Soria
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain
| | - R Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain
| | - F Bastida
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, E-30100, Espinardo, Murcia, Spain
| | - I Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain.
| |
Collapse
|
20
|
Short-Term Effect of Green Waste and Sludge Amendment on Soil Microbial Diversity and Volatile Organic Compound Emissions. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1010010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Soil amendments with organic waste products (OWPs) have been widely supported in Europe to improve soil fertility, causing wide changes in the microbial community structure and diversity, especially in the short-term period. Those changes are known to affect the volatile organic compound (VOC) emissions by soil. This work aimed to characterize, in terms of quantity and composition, the effect of green waste and sludge (GWS) application on soil VOC emissions and microbial community 49 h after the last GWS application. Two different soil samples were compared to test the effect of the soil history on VOC emissions and microbial communities. For this reason, we chose a soil that received GWS input for 20 years (GWS sample) and one that did not receive any organic input during the same period (CN sample). Furthermore, samples were manipulated to generate three microbial dilution diversity gradients (low, medium, and high). Results showed that Bacteroidetes phyla took advantage of the GWS application in all samples, increasing their relative abundance by 22% after 49 h, while the Proteobacteria phylum was penalized by the GWS amendment, passing from 58% to 49% relative abundance 49 h after the GWS application. Microbial structure differences between microbial diversity dilution levels remained even after the GWS application. GWS amendment induced a change in the emitted VOC profiles, especially in samples used to receiving GWS. GWS amendment doubled the VOC emissions from samples used to receiving GWS after 49 h. Finally, the microbial community was strongly correlated to the VOC emissions. Firmicutes, Proteobacteria, Actinobacteria, and Crenarchaeota were positively correlated (Pearson coefficient > 0.6), while other phyla, such as Bacteroidetes and Verrucomicrobia, were found to be negatively correlated (Pearson coefficient < −0.6) to the VOC emissions. After the addition of GWS, these correlations shifted from positive to negative and from negative to positive.
Collapse
|
21
|
Daraz U, Li Y, Sun Q, Zhang M, Ahmad I. Inoculation of Bacillus spp. Modulate the soil bacterial communities and available nutrients in the rhizosphere of vetiver plant irrigated with acid mine drainage. CHEMOSPHERE 2021; 263:128345. [PMID: 33297270 DOI: 10.1016/j.chemosphere.2020.128345] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 05/16/2023]
Abstract
Acid mine drainage (AMD) is one of an important pollution sources associated with mining activities and often inhibits plant growth. Plant growth promoting bacteria has received extensive attention for enhancing adaptability of plants growing in AMD polluted soils. The present study investigated the effect of plant growth promoting Bacillus spp. (strains UM5, UM10, UM13, UM15 and UM20) to improve vetiver (Chrysopogon zizanioides L.) adaptability in a soil irrigated with 50% AMD. Bacillus spp. exhibited P-solubilization, IAA and siderophore production. The Bacillus spp. strains UM10 and UM13 significantly increased shoot (4.2-2.5%) and root (3.4-1.9%) biomass in normal and AMD-impacted soil, respectively. Bacillus sp. strain UM20 significantly increased soil AP (379.93 mg/kg) while strain UM13 increased TN (1501.69 mg/kg) and WEON (114.44 mg/kg) than control. Proteobacteria, Chloroflexi, Acidobacteria and Bacteroidetes are the dominant phyla, of which Acidobacteria (12%) and Bacteroidetes (8.5%) were dominated in soil inoculated with Bacillus sp. strain UM20 while Proteobacteria (70%) in AMD soil only. However, the Chao1 and evenness indices were significantly increased in soil inoculated with Bacillus sp. strain UM13. Soil pH, AP and N fractions were positively correlated with the inoculation of bacterial strains UM13 and UM20. Plant growth promoting Bacillus spp. strains UM13 and UM20 were the main contributors to the variations in the rhizosphere bacterial community structure, improving soil available P, TN, WEON, NO3--N thus could be a best option to promote C. zizanioides adaptability in AMD-impacted soils.
Collapse
Affiliation(s)
- Umar Daraz
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, 230601, China; Key Laboratory of Wetland Ecological Protection and Restoration, China; Mining Environmental Restoration and Wetland Ecological Security Collaborative Innovation Center, China
| | - Yang Li
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, 230601, China; Key Laboratory of Wetland Ecological Protection and Restoration, China; Mining Environmental Restoration and Wetland Ecological Security Collaborative Innovation Center, China
| | - Qingye Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, 230601, China; Key Laboratory of Wetland Ecological Protection and Restoration, China; Mining Environmental Restoration and Wetland Ecological Security Collaborative Innovation Center, China.
| | - Mingzhu Zhang
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province, 230601, China; Key Laboratory of Wetland Ecological Protection and Restoration, China; Mining Environmental Restoration and Wetland Ecological Security Collaborative Innovation Center, China
| | - Iftikhar Ahmad
- Department of Environmental Sciences, COMSATS University Islamabad Vehari-Campus, Vehari, 61100, Pakistan
| |
Collapse
|
22
|
Montes de Oca-Vásquez G, Solano-Campos F, Vega-Baudrit JR, López-Mondéjar R, Vera A, Moreno JL, Bastida F. Organic amendments exacerbate the effects of silver nanoparticles on microbial biomass and community composition of a semiarid soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140919. [PMID: 32711321 DOI: 10.1016/j.scitotenv.2020.140919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/24/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Increased utilization of silver nanoparticles (AgNPs) can result in an accumulation of these particles in the environment. The potential detrimental effects of AgNPs in soil may be associated with the low fertility of soils in semiarid regions that are usually subjected to restoration through the application of organic amendments. Microbial communities are responsible for fundamental processes related to soil fertility, yet the potential impacts of low and realistic AgNPs concentrations on soil microorganisms are still unknown. We studied the effects of realistic citrate-stabilized AgNPs concentrations (0.015 and 1.5 μg kg-1) at two exposure times (7 and 30 days) on a sandy clay loam Mediterranean soil unamended (SU) and amended with compost (SA). We assessed soil microbial biomass (microbial fatty acids), soil enzyme activities (urease, β-glucosidase, and alkaline phosphatase), and composition of the microbial community (bacterial 16S rRNA gene and fungal ITS2 sequencing) in a microcosm experiment. In the SA, the two concentrations of AgNPs significantly decreased the bacterial biomass after 7 days of incubation. At 30 days of incubation, only a significant decrease in the Gram+ was observed at the highest AgNPs concentration. In contrast, in the SU, there was a significant increase in bacterial biomass after 30 days of incubation at the lowest AgNPs concentration. Overall, we found that fungal biomass was more resistant to AgNPs than bacterial biomass, in both SA and SU. Further, the AgNPs changed the composition of the soil bacterial community in SA, the relative abundance of some bacterial taxa in SA and SU, and fungal richness in SU at 30 days of incubation. However, AgNPs did not affect the activity of extracellular enzymes. This study demonstrates that the exposure time and organic amendments modulate the effects of realistic concentrations of AgNPs in the biomass and composition of the microbial community of a Mediterranean soil.
Collapse
Affiliation(s)
- Gabriela Montes de Oca-Vásquez
- National Nanotechnology Laboratory, National Center for High Technology, 10109 Pavas, San José, Costa Rica; Doctorado en Ciencias Naturales para el Desarrollo (DOCINADE), Instituto Tecnológico de Costa Rica, Universidad Nacional, Universidad Estatal a Distancia, Costa Rica.
| | - Frank Solano-Campos
- School of Biological Sciences, Universidad Nacional, Campus Omar Dengo, 86-3000 Heredia, Costa Rica
| | - José R Vega-Baudrit
- National Nanotechnology Laboratory, National Center for High Technology, 10109 Pavas, San José, Costa Rica; Laboratory of Polymer Science and Technology, School of Chemistry, Universidad Nacional, Campus Omar Dengo, 86-3000 Heredia, Costa Rica
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, Praha 4 14220, Czech Republic
| | - Alfonso Vera
- CEBAS-CSIC. Department of Soil and Water Conservation. Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - José L Moreno
- CEBAS-CSIC. Department of Soil and Water Conservation. Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - Felipe Bastida
- CEBAS-CSIC. Department of Soil and Water Conservation. Campus Universitario de Espinardo, 30100 Murcia, Spain
| |
Collapse
|
23
|
Yu J, Pavia MJ, Deem LM, Crow SE, Deenik JL, Penton CR. DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil. Front Microbiol 2020; 11:587972. [PMID: 33329461 PMCID: PMC7717982 DOI: 10.3389/fmicb.2020.587972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/08/2020] [Indexed: 12/03/2022] Open
Abstract
The functions and interactions of individual microbial populations and their genes in agricultural soils amended with biochar remain elusive but are crucial for a deeper understanding of nutrient cycling and carbon (C) sequestration. In this study, we coupled DNA stable isotope probing (SIP) with shotgun metagenomics in order to target the active community in microcosms which contained soil collected from biochar-amended and control plots under napiergrass cultivation. Our analyses revealed that the active community was composed of high-abundant and low-abundant populations, including Actinobacteria, Proteobacteria, Gemmatimonadetes, and Acidobacteria. Although biochar did not significantly shift the active taxonomic and functional communities, we found that the narG (nitrate reductase) gene was significantly more abundant in the control metagenomes. Interestingly, putative denitrifier genomes generally encoded one gene or a partial denitrification pathway, suggesting denitrification is typically carried out by an assembly of different populations within this Oxisol soil. Altogether, these findings indicate that the impact of biochar on the active soil microbial community are transient in nature. As such, the addition of biochar to soils appears to be a promising strategy for the long-term C sequestration in agricultural soils, does not impart lasting effects on the microbial functional community, and thus mitigates un-intended microbial community shifts that may lead to fertilizer loss through increased N cycling.
Collapse
Affiliation(s)
- Julian Yu
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Michael J. Pavia
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- Swette Center for Environmental Biotechnology, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Lauren M. Deem
- Natural Resources and Environmental Management, University of Hawai‘i at Mânoa, Honolulu, HI, United States
| | - Susan E. Crow
- Natural Resources and Environmental Management, University of Hawai‘i at Mânoa, Honolulu, HI, United States
| | - Jonathan L. Deenik
- Tropical Plant and Soil Sciences, University of Hawai‘i at Mânoa, Honolulu, HI, United States
| | - Christopher Ryan Penton
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
| |
Collapse
|
24
|
Tartaglia M, Bastida F, Sciarrillo R, Guarino C. Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights. Int J Mol Sci 2020; 21:ijms21228455. [PMID: 33187080 PMCID: PMC7697097 DOI: 10.3390/ijms21228455] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Soil is a complex matrix where biotic and abiotic components establish a still unclear network involving bacteria, fungi, archaea, protists, protozoa, and roots that are in constant communication with each other. Understanding these interactions has recently focused on metagenomics, metatranscriptomics and less on metaproteomics studies. Metaproteomic allows total extraction of intracellular and extracellular proteins from soil samples, providing a complete picture of the physiological and functional state of the “soil community”. The advancement of high-performance mass spectrometry technologies was more rapid than the development of ad hoc extraction techniques for soil proteins. The protein extraction from environmental samples is biased due to interfering substances and the lower amount of proteins in comparison to cell cultures. Soil sample preparation and extraction methodology are crucial steps to obtain high-quality resolution and yields of proteins. This review focuses on the several soil protein extraction protocols to date to highlight the methodological challenges and critical issues for the application of proteomics to soil samples. This review concludes that improvements in soil protein extraction, together with the employment of ad hoc metagenome database, may enhance the identification of proteins with low abundance or from non-dominant populations and increase our capacity to predict functional changes in soil.
Collapse
Affiliation(s)
- Maria Tartaglia
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy; (M.T.); (R.S.)
| | - Felipe Bastida
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100 Murcia, Spain;
| | - Rosaria Sciarrillo
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy; (M.T.); (R.S.)
| | - Carmine Guarino
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy; (M.T.); (R.S.)
- Correspondence: ; Tel.: +39-824-305145
| |
Collapse
|
25
|
Halter M, Vaisvil B, Kapatral V, Zahn J. Organic farming practices utilizing spent microbial biomass from an industrial fermentation facility promote transition to copiotrophic soil communities. J Ind Microbiol Biotechnol 2020; 47:1005-1018. [PMID: 33098066 DOI: 10.1007/s10295-020-02318-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/01/2020] [Indexed: 12/25/2022]
Abstract
Organic farming has become more prevalent in recent years as consumer demand for organic food and fiber has rapidly grown. Until recently, organic fertilizers and soil amendments have largely been based on the practices of returning crop residues, manures and related agricultural wastes back to crop production areas. One rapidly growing segment in commercial organic fertilizer development is the use of spent microbial biomass (SMB) from industrial fermentation processes. While SMB is widely accepted in many organic farming systems (OFS), little is known concerning the effectiveness, environmental impact, and influence on prokaryotic communities in soils receiving this treatment. In this study, a comparative analysis of bacterial communities associated with OFS and conventional farming systems was performed over a growing season for a field containing yellow dent corn (Zea mays). A statistically significant increase in microbial population α-diversity, along with a strong recruitment of Proteobacteria and Actinobacteria populations, was observed in soils treated with SMB when compared to areas in the field that utilized conventional farmer practices. These phyla are members of the copiotrophic subgroup, and considered a signature for the use of traditional organic fertilizers. These results provide valuable new information that SMB functions similarly to traditional organic fertilizers in promoting a high level of functional prokaryotic diversity and plant growth-promoting bacteria, but in contrast do not contribute directly to viable microorganisms in the soil due to the sterilization of SMB prior to land application.
Collapse
Affiliation(s)
- Mathew Halter
- DuPont Tate & Lyle BioProducts, 198 Blair Bend Drive, Loudon, TN, 37774, USA.,Synthorx, 11099 N. Torrey Pines Road, Suite 190, La Jolla, CA, 92037, USA
| | | | | | - James Zahn
- DuPont Tate & Lyle BioProducts, 198 Blair Bend Drive, Loudon, TN, 37774, USA.
| |
Collapse
|
26
|
Rodríguez-Berbel N, Ortega R, Lucas-Borja ME, Solé-Benet A, Miralles I. Long-term effects of two organic amendments on bacterial communities of calcareous mediterranean soils degraded by mining. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 271:110920. [PMID: 32579515 DOI: 10.1016/j.jenvman.2020.110920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
The application of organic amendments to improve the chemical and biological properties of degraded soils from calcareous quarries is necessary to accelerate restoration processes. The aim of this study is to assess the success of different restoration treatments in the long-term using two organic amendments (sewage sludge from urban waste water (SS) and compost from domestic solid waste (CW)). The chemical properties and bacterial communities of restored soils were compared with unamended soils (NA) and surrounding natural soils (NS) from a limestone quarry in a semi-arid ecosystem. After 10 years of the addition of organic amendments, the abundance of soil bacteria, diversity, and taxonomic composition at the phylum and genus level in each soil type was analysed by rRNA 16 S amplification (PCR), sequencing using Illumina, and comparison with the SILVA database using QIIME2 software. The relationships between soil bacterial taxa and chemical soil properties (pH, electrical conductivity (EC), total organic carbon (TOC), and total nitrogen content (TN)) were also studied, as well as the interrelations between soil bacterial taxa at the genus level or the next upper taxonomic level identified. The organic amendments changed the chemical properties of the restored soils, influencing the microbial communities of the restored soils. CW treatment was the organic amendment that most resembled NS, favouring in the long-term a greater diversity and proliferation of bacteria. Several bacterial communities, more abundant in NA and CW soils, were strongly correlated with each other (Craurococcus, Phaselicystis, Crossiella, etc.), forming a bacterial co-occurrence pattern (Co-occurrence pattern 1). Those bacteria showed high significant positive correlations with TOC, TN, and EC and negative correlations with the soil pH. In contrast, NA soils presented other groups of bacterial communities (Co-occurrence pattern 2) represented by Sphingomonas, Rubellimicrobium, Noviherbaspirillum, Psychroglaciecola and Caenimonas, which showed high significant positive correlations with soil pH and negative correlations with TOC, TN, and EC. The distance-based redundancy analysis indicated that SS soils remained in an intermediate stage of chemical and biological quality between NS and NA soils. Our results demonstrate that soil chemical properties and soil bacterial communities significantly changed with organic amendments in calcareous Mediterranean soils degraded by mining.
Collapse
Affiliation(s)
- N Rodríguez-Berbel
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
| | - R Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
| | - M E Lucas-Borja
- Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha, Campus Universitario, 02071, Albacete, Spain
| | - A Solé-Benet
- EEZA-CSIC, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, Carretera de Sacramento S/n, 04120, La Cañada de San Urbano, Almería, Spain
| | - I Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain.
| |
Collapse
|
27
|
Omirou M, Anastopoulos I, Fasoula DA, Ioannides IM. The effect of chemical and organic N inputs on N 2O emission from rain-fed crops in Eastern Mediterranean. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 270:110755. [PMID: 32721287 DOI: 10.1016/j.jenvman.2020.110755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/24/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
Nitrogen has a significant contribution to global warming and its reduction in agriculture is expected to reduce N2O emissions having however adverse effects on the productivity of agricultural ecosystems. Maintaining systems productivity with alternative N sources i.e manure and composts could be a strategy also to mitigate N2O emissions. In this paper, we present the effect of different N sources (organic and chemical) on field N2O emissions and how these emissions are associated with soil available N forms (NH4+ and NO3-) in three different rain-fed crops namely barley, pea and vetch grown in Cyprus for two growing seasons. The daily emissions ranged from -3.11 to 12.3 g N-N2O/ha/day, while cumulative emissions ranged from 119 g N-N2O/ha to 660 g N-N2O/ha depending on crop and nitrogen source type. The emissions showed a seasonal pattern and WFPS has been identified as a critical soil parameter controlling daily N2O emissions. The daily N2O fluxes in the current study derives mainly from nitrification irrespectively crop type or nitrogen source type. Specific emission factors for each crop cultivated under different N source type were calculated and ranged from 0.03% ± 0.02-0.34% ± 0.09. The application of manure and chemical fertilizers cause similar intensity of N2O emissions while compost exhibited the lower emission factors. These findings suggest that composts could be integrated in a nutrient management strategy of rain-fed crops with less N2O emissions. The high background emissions found suggest also that other factors than external inputs are associated with N2O emissions and further studies including the response of microbial community structure and their contribution and association with N2O emissions.
Collapse
Affiliation(s)
- Michalis Omirou
- Department of Agrobiotechnology, Agricultural Research Institute, P.O.Box 22016, Nicosia, 1516, Cyprus.
| | - Ioannis Anastopoulos
- University of Cyprus, Department of Chemistry, P.O.Box 20537, Nicosia, 1678, Cyprus
| | - Dionysia A Fasoula
- Department of Plant Breeding, Agricultural Research Institute, P.O.Box 22016, Nicosia, 1516, Cyprus
| | - Ioannis M Ioannides
- Department of Agrobiotechnology, Agricultural Research Institute, P.O.Box 22016, Nicosia, 1516, Cyprus.
| |
Collapse
|
28
|
Nero BF. Phytoremediation of petroleum hydrocarbon-contaminated soils with two plant species: Jatropha curcas and Vetiveria zizanioides at Ghana Manganese Company Ltd. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2020; 23:171-180. [PMID: 32805144 DOI: 10.1080/15226514.2020.1803204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The study investigated the effects of Jatropha curcas (JC) and Vetiveria zizanioides (VZ) on hydrocarbon concentration levels in mine spoils. A 2 × 2 × 3 factorial arrangement of treatments in a completely randomized design with 3 replications was adopted. With compost amendments, JC caused 78.8 and 82.2% and VZ caused 51.1 and 39.7% decline in soil TPH and TOG concentrations, respectively after 16 weeks. Compost amendments significantly reduced TOG and TPH concentrations compared to the other treatments in both JC and VZ (p < 0.0001). However, the effect of species on TOG and TPH concentrations were marginally significant (p = 0.081 and p < 0.006, respectively). Growth in height, collar diameter and number of leaves in JC were significantly higher in the compost amendment compared to the fertilizer and control treatments (p < 0.0001). Number of leaves (p = 0.009) and collar diameter growth (p = 0.010) were significantly lower in contaminated soils compared to non-contaminated soils. Furthermore, only the number of tillers in Vetiver was significantly influenced by the soil amendments (p = 0.003) and the soil hydrocarbon levels (p = 0.048). It is concluded that phytoremediation particularly with JC is an alternate means to reducing soil hydrocarbon concentration levels. However, soils must be amended with compost for effective remediation and rapid, vigorous, early growth of plants.
Collapse
Affiliation(s)
- Bertrand Festus Nero
- College of Agriculture and Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| |
Collapse
|
29
|
Huang R, Chen P, Wang X, Li H, Zuo L, Zhang Y, Li L. Structural variability and niche differentiation of the rhizosphere and endosphere fungal microbiome of Casuarina equisetifolia at different ages. Braz J Microbiol 2020; 51:1873-1884. [PMID: 32661898 DOI: 10.1007/s42770-020-00337-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/08/2020] [Indexed: 10/23/2022] Open
Abstract
BACKGROUND Casuarina equisetifolia is one of the most important artificially planted protective forests along the coast in southern China for windbreaks, soil erosion, and sand dune stabilization. Self-renewing of C. equisetifolia is very limited, which might be caused by low soil nutrient levels and reduced microbial activity. METHODS Use of high-throughput sequencing of the 18S rDNA to investigate the microbial communities from the rhizosphere and root endosphere of C. equisetifolia in young-aged, intermediate-aged, and mature-aged forests. RESULTS Our results indicate that the diversity of rhizosphere fungal microbiomes in field-grown C. equisetifolia is much lower than that of the endosphere microbiomes. Bioinformatic analysis showed that rhizocompartments produce the strongest differentiation of rhizosphere and endosphere communities. Notably, the distribution of rhizosphere fungi communities was significantly influenced by the environmental factors, not by forest ages. CONCLUSIONS The presented study suggests that the rhizocompartments and environmental factors, rather than forest ages, determine the diversities of fungal community.
Collapse
Affiliation(s)
- Rui Huang
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, 571158, Hainan, China
| | - Pan Chen
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, 571158, Hainan, China
| | - Xuan Wang
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, 571158, Hainan, China
| | - Huimin Li
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, 571158, Hainan, China
| | - Linzhi Zuo
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, 571158, Hainan, China
| | - Yaqian Zhang
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, 571158, Hainan, China
| | - Lei Li
- College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, 571158, Hainan, China.
| |
Collapse
|
30
|
Zou Y, Yan J, Hou S, Yi Y, Cui B. Intensive land uses modify assembly process and potential metabolic function of edaphic bacterial communities in the Yellow River Delta, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137713. [PMID: 32325607 DOI: 10.1016/j.scitotenv.2020.137713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
Coastal reclamation is a global threat to natural ecosystems, disturbing biological community structure, diversity and ecological function through habitat conversion. We have limited insights into the changes brought about by coastal reclamation for different land-use types. We used the Yellow River Delta (YRD) as a model because it is a region with intensive land reclamation, and we investigated the structural and functional variations of bacterial communities and their relations to edaphic properties under different land-use types. Our results showed that the high soil organic carbon (SOC), nitrate concentrations and salinity were found in oil field, aquaculture pond and salt pan, respectively, and low values in natural wetland. Land use was found to have significant influence on bacterial community diversity. To investigate the phylogenetic conservation of specific traits, we analyzed the relationship between soil bacterial assembly processes and edaphic properties. Bacterial traits phylogenetically conserved, and differs in depth. Our findings suggest that SOC served as a deep trait due to it negative correlation with deeper branches of phylogenetic clustering, while nitrate functioned as a shallow trait due to its positive correlation with phylogenetic clustering at finer branches. Soil salinity acted as a complex trait effected on both finer and deeper branches. Further potential functional gene co-occurrence network analysis revealed that land reclamation induced shifts of metabolic function by altering the functional gene connectivity. We found that the photosynthesis pathway was enriched in hub modules related to oil field (OF), while methane metabolism was enriched in hub modules linked to sea cucumber pond (CP1). In addition, two-component systems (TCS) were enriched with nitrate, ammonia, SOC and salinity-related modules. Therefore, our study highlights the importance of integrating multi-function and multi-process identification and prediction of coastal diverse reclamation impacts on coastal ecosystems.
Collapse
Affiliation(s)
- Yuxuan Zou
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, 100875 Beijing, China
| | - Jiaguo Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, 100875 Beijing, China
| | - Shengwei Hou
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yujun Yi
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, 100875 Beijing, China
| | - Baoshan Cui
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, 100875 Beijing, China.
| |
Collapse
|
31
|
Dong Y, Gao J, Wu Q, Ai Y, Huang Y, Wei W, Sun S, Weng Q. Co-occurrence pattern and function prediction of bacterial community in Karst cave. BMC Microbiol 2020; 20:137. [PMID: 32471344 PMCID: PMC7257168 DOI: 10.1186/s12866-020-01806-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 04/28/2020] [Indexed: 01/20/2023] Open
Abstract
Background Karst caves are considered as extreme environments with nutrition deficiency, darkness, and oxygen deprivation, and they are also the sources of biodiversity and metabolic pathways. Microorganisms are usually involved in the formation and maintenance of the cave system through various metabolic activities, and are indicators of changes environment influenced by human. Zhijin cave is a typical Karst cave and attracts tourists in China. However, the bacterial diversity and composition of the Karst cave are still unclear. The present study aims to reveal the bacterial diversity and composition in the cave and the potential impact of tourism activities, and better understand the roles and co-occurrence pattern of the bacterial community in the extreme cave habitats. Results The bacterial community consisted of the major Proteobacteria, Actinobacteria, and Firmicutes, with Proteobacteria being the predominant phylum in the rock, soil, and stalactite samples. Compositions and specialized bacterial phyla of the bacterial communities were different among different sample types. The highest diversity index was found in the rock samples with a Shannon index of 4.71. Overall, Zhijin cave has relatively lower diversity than that in natural caves. The prediction of function showed that various enzymes, including ribulose-bisphosphate carboxylase, 4-hydroxybutyryl-CoA dehydratase, nitrogenase NifH, and Nitrite reductase, involved in carbon and nitrogen cycles were detected in Zhijin cave. Additionally, the modularity indices of all co-occurrence network were greater than 0.40 and the species interactions were complex across different sample types. Co-occurring positive interactions in the bacteria groups in different phyla were also observed. Conclusion These results uncovered that the oligotrophic Zhijin cave maintains the bacterial communities with the diverse metabolic pathways, interdependent and cooperative co-existence patterns. Moreover, as a hotspot for tourism, the composition and diversity of bacterial community are influenced by tourism activities. These afford new insights for further exploring the adaptation of bacteria to extreme environments and the conservation of cave ecosystem.
Collapse
Affiliation(s)
- Yiyi Dong
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, Guizhou, China.,CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Yilang Ai
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Yu Huang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Wenzhang Wei
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, Guizhou, China.,Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, 361021, Fujian, China
| | - Shiyu Sun
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, Guizhou, China.
| |
Collapse
|
32
|
Salhi A, Benabdelouahab T, Martin-Vide J, Okacha A, El Hasnaoui Y, El Mousaoui M, El Morabit A, Himi M, Benabdelouahab S, Lebrini Y, Boudhar A, Casas Ponsati A. Bridging the gap of perception is the only way to align soil protection actions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 718:137421. [PMID: 32105933 DOI: 10.1016/j.scitotenv.2020.137421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/01/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
Science is the seed of a decent life, with which we sow hope in the present and which we irrigate with the perfecting of good deeds. It is even crucial in the Mediterranean southern frontiers where the cultural erosion dissolves the structure of a society abandoned by the arms and brains of its youth. Soil-water-vegetation crisis should not be underestimated; coupled with socioeconomic congestion it would lead to an irremediable crash. Here, we show that the first and most difficult step to face soil degradation is to cultivate the right idea and develop it into a well-established community culture. We found in northern Morocco that 94.5% of farmers have no qualification and 82.6% of them act in a way that worsens soil degradation even if they are aware of the severity of the problem. This confused perception of ideas originates inappropriate labour behaviours non-aligned with public actions. Our results show that the impact of this is a high potential regional erosion rate of 27.7 t/ha/year which is equivalent to a massive potential gross amount of soil loss of 44.3 Mt/year. We show that this leads to an overall vegetation decrease related mainly to the anthropogenic pressure then to climate and lithology. We anticipate that the solution must be comprehensive, participatory, strategic and innovative, led by education and scientific research (Citizen Science) and involving all actors equally. In its broad context, the only path to achieve the coordination and alignment of actions would be through a gradual change of perception and involvement based on a time-consuming culture of assimilation and acceptance rather than a culture of rapid reform.
Collapse
Affiliation(s)
- Adil Salhi
- Geography and Development Group, Abdelmalek Essaadi University, Martil, Morocco.
| | | | | | - Abdelmonaim Okacha
- Geography and Development Group, Abdelmalek Essaadi University, Martil, Morocco
| | - Yassin El Hasnaoui
- Geography and Development Group, Abdelmalek Essaadi University, Martil, Morocco
| | - Mhamed El Mousaoui
- Geography and Development Group, Abdelmalek Essaadi University, Martil, Morocco
| | | | - Mahjoub Himi
- Economic and Environmental Geology and Hydrology Group, University of Barcelona, Barcelona, Spain.
| | - Sara Benabdelouahab
- Economic and Environmental Geology and Hydrology Group, University of Barcelona, Barcelona, Spain.
| | - Youssef Lebrini
- National Institute of Agronomic Research, Rabat, Morocco; Water Resource Management, Valorisation and Remote Sensing Group, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Abdelghani Boudhar
- Water Resource Management, Valorisation and Remote Sensing Group, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Albert Casas Ponsati
- Economic and Environmental Geology and Hydrology Group, University of Barcelona, Barcelona, Spain.
| |
Collapse
|
33
|
Xu G, Long Z, Ren P, Ren C, Cao Y, Huang Y, Hu S. Differential responses of soil hydrolytic and oxidative enzyme activities to the natural forest conversion. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:136414. [PMID: 32045769 DOI: 10.1016/j.scitotenv.2019.136414] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/28/2019] [Accepted: 12/28/2019] [Indexed: 06/10/2023]
Abstract
Effects of natural forest conversion (NFC) on soil nutrient turnover are substantially mediated by soil microbial extracellular hydrolytic enzymatic activities (Hy-EEAs) and oxidative enzymatic activities (Ox-EEAs). Yet it remains largely unknown the indicative links between soil Hy- and Ox-EEAs and soil carbon (C), nitrogen (N) and phosphorus (P) supplies based on economic theories of microbial metabolism under NFC. Here we used a meta-analysis approach to synthesize the responses of the soil C-, N-, P-degrading Hy-EEAs and Ox-EEAs, soil microbial biomass, soil organic C, total N, P and available P parameters to natural forest conversion from 51 peer-reviewed studies. Our results showed that NFC notably decreased soil Hy-EEAs but statistically insignificant reduction of soil Ox-EEAs. The changes of soil Hy- and Ox-EEAs were significantly and positively associated with soil organic C, available P as well as microbial biomass C and N but significantly and negatively correlated with soil pH, whereas the changes of soil C/N impacted on soil Ox-EEAs remarkably but not for soil Hy-EEAs. The depletion of soil organic carbon stimulated soil microbial secretion of Hy- and Ox-EEAs. The soil total N scarcity only provoked soil microbial Hy-EEAs rather than Ox-EEAs. The soil total P dearth quickened the soil Ox-EEAs, however, the plenitude of soil available P suppressed soil Hy- and Ox-EEAs. Moreover, the eco-enzymatic stoichiometry of soil Hy-EEAs indicated that soil N and P nutrient limitation after NFC restricted soil microbial N- and P-acquiring enzymes secretion, which ultimately reduced resources availability for C acquisition. Altogether, the distinct responses of soil Hy- and Ox-EEAs depended on substrate availability peculiarly for soil N and P gains of microorganisms for further enzymatic ability on soil C decomposition and highlighted the abundant or absent supply of soil N and P for positive or negative enzymatic activities on metabolic requirement of soil edaphons.
Collapse
Affiliation(s)
- Gang Xu
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China; Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
| | - Zhijian Long
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Peng Ren
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Chengjie Ren
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ying Cao
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Yan Huang
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Shanglian Hu
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China.
| |
Collapse
|
34
|
Chen J, Arafat Y, Ud Din I, Yang B, Zhou L, Wang J, Letuma P, Wu H, Qin X, Wu L, Lin S, Zhang Z, Lin W. Nitrogen Fertilizer Amendment Alter the Bacterial Community Structure in the Rhizosphere of Rice ( Oryza sativa L.) and Improve Crop Yield. Front Microbiol 2019; 10:2623. [PMID: 31798559 PMCID: PMC6868037 DOI: 10.3389/fmicb.2019.02623] [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: 03/18/2019] [Accepted: 10/28/2019] [Indexed: 01/01/2023] Open
Abstract
Availability of nitrogen (N) in soil changes the composition and activities of microbial community, which is critical for the processing of soil organic matter and health of crop plants. Inappropriate application of N fertilizer can alter the rhizosphere microbial community and disturb the soil N homeostasis. The goal of this study was to assess the effect of different ratio of N fertilizer at various early to late growth stages of rice, while keeping the total N supply constant on rice growth performance, microbial community structure, and soil protein expression in rice rhizosphere. Two different N regimes were applied, i.e., traditional N application (NT) consists of three sessions including 60, 30 and 10% at pre-transplanting, tillering and panicle initiation stages, respectively, while efficient N application (NF) comprises of four sessions, i.e., 30, 30, 30, and 10%), where the fourth session was extended to anthesis stage. Soil metaproteomics combined with Terminal Restriction Fragment Length Polymorphism (T-RFLP) were used to determine the rhizosphere biological process. Under NF application, soil enzymes, nitrogen utilization efficiency and rice yield were significantly higher compared to NT application. T-RFLP and qPCR analysis revealed differences in rice rhizosphere bacterial diversity and structure. NF significantly decreased the specific microbes related to denitrification, but opposite result was observed for bacteria associated with nitrification. Furthermore, soil metaproteomics analysis showed that 88.28% of the soil proteins were derived from microbes, 5.74% from plants, and 6.25% from fauna. Specifically, most of the identified microbial proteins were involved in carbohydrate, amino acid and protein metabolisms. Our experiments revealed that NF positively regulates the functioning of the rhizosphere ecosystem and further enabled us to put new insight into microbial communities and soil protein expression in rice rhizosphere.
Collapse
Affiliation(s)
- Jun Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yasir Arafat
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Genetic Breeding and Comprehensive Utilization of the Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Israr Ud Din
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Bo Yang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liuting Zhou
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juanying Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Puleng Letuma
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hongmiao Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xianjin Qin
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Linkun Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhixing Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
35
|
Dang Q, Tan W, Zhao X, Li D, Li Y, Yang T, Li R, Zu G, Xi B. Linking the response of soil microbial community structure in soils to long-term wastewater irrigation and soil depth. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 688:26-36. [PMID: 31233911 DOI: 10.1016/j.scitotenv.2019.06.138] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/04/2019] [Accepted: 06/08/2019] [Indexed: 05/08/2023]
Abstract
Irrigation with treated wastewater (TWW) has become a prevailing agricultural practice due to the scarcity of fresh water resources, which may have a significant impact on the microbial communities that are critical to many biogeochemical processes in soils. However, it is unclear whether there are links between soil microbial responses to long-term irrigation with different sources of wastewater and soil depth. Here we assess the influence of treated domestic (DTWW), leather industry (LTWW) and pharmaceutical (PTWW) wastewater on microbial communities in vertical soil profiles using high-throughput sequencing based on 16S rRNA and internal transcribed spacer (ITS) gene profiling. We found that microbial α-diversity in the vertical profiles of soils was significantly influenced by TWW irrigation. Bacteria and fungi in different soil depths showed distinct responses to TWW; irrigation with TWW markedly increased abundance of bacterial OTUs and inhibited abundance of fungal OTUs. β-diversity analysis showed that the effect of TWW irrigation on microbial communities was greater than the effect of soil depth, and microbes in subsurface soil were more sensitive to different sources of irrigation water. We also found that, based on β-diversity analysis, irrigation with treated industrial wastewater, including LTWW and PTWW, had a greater impact on microbial community structures than DTWW. TWW irrigation significantly affected the composition of indigenous soil microbial communities at different depths and might introduce exogenous microbes into the soil environment. Our work explicitly demonstrates the vertical responses of bacterial and fungal communities in soils to irrigation with TWW from different sources, which can provides insights into the microbial-dominated geochemical processes from the perspective of the entire soil profile under the context of wastewater irrigation.
Collapse
Affiliation(s)
- Qiuling Dang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xinyu Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Dan Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yanping Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Tianxue Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Renfei Li
- State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Guofeng Zu
- Groundwater Pollution Control and Remediation Industry Alliance, Beijing 100012, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| |
Collapse
|
36
|
Celestina C, Wood JL, Manson JB, Wang X, Sale PWG, Tang C, Franks AE. Microbial communities in top- and subsoil of repacked soil columns respond differently to amendments but their diversity is negatively correlated with plant productivity. Sci Rep 2019; 9:8890. [PMID: 31222122 PMCID: PMC6586782 DOI: 10.1038/s41598-019-45368-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 05/31/2019] [Indexed: 11/22/2022] Open
Abstract
Organic and inorganic amendments with equivalent nutrient content may have comparable fertilizer effects on crop yield, but their effects on the soil microbial community and subsequent plant-soil-microbe interactions in this context are unknown. This experiment aimed to understand the relationship between soil microbial communities, soil physicochemical characteristics and crop performance after addition of amendments to soil. Poultry litter and synthetic fertilizer with balanced total nitrogen (N) content equivalent to 1,200 kg ha−1 were added to the topsoil (0–10 cm) or subsoil layer (20–30 cm) of repacked soil columns. Wheat plants were grown until maturity. Soil samples were taken at Zadoks 87–91 (76 days after sowing) for analysis of bacterial and fungal communities using 16S and ITS amplicon sequencing. The interaction between amendment type and placement depth had significant effects on bacterial and fungal community structure and diversity in the two soil layers. Addition of poultry litter and fertilizer stimulated or suppressed different taxa in the topsoil and subsoil leading to divergence of these layers from the untreated control. Both amendments reduced microbial community richness, diversity and evenness in the topsoil and subsoil compared to the nil-amendment control, with these reductions in diversity being consistently negatively correlated with plant biomass (root and shoot weight, root length, grain weight) and soil fertility (soil NH4+, shoot N). These results indicate that in this experimental system, the soil microbial diversity was correlated negatively with plant productivity.
Collapse
Affiliation(s)
- Corinne Celestina
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia.,Centre for Future Landscapes, La Trobe University, Bundoora, VIC 3086, Australia
| | - Jennifer L Wood
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia.,Centre for Future Landscapes, La Trobe University, Bundoora, VIC 3086, Australia
| | - James B Manson
- Department of Animal, Plant and Soil Sciences, AgriBio the Centre for AgriBiosciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Xiaojuan Wang
- Department of Animal, Plant and Soil Sciences, AgriBio the Centre for AgriBiosciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Peter W G Sale
- Department of Animal, Plant and Soil Sciences, AgriBio the Centre for AgriBiosciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, AgriBio the Centre for AgriBiosciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia. .,Centre for Future Landscapes, La Trobe University, Bundoora, VIC 3086, Australia.
| |
Collapse
|
37
|
Liu D, Keiblinger KM, Leitner S, Wegner U, Zimmermann M, Fuchs S, Lassek C, Riedel K, Zechmeister-Boltenstern S. Response of Microbial Communities and Their Metabolic Functions to Drying⁻Rewetting Stress in a Temperate Forest Soil. Microorganisms 2019; 7:E129. [PMID: 31086038 PMCID: PMC6560457 DOI: 10.3390/microorganisms7050129] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 11/23/2022] Open
Abstract
Global climate change is predicted to alter drought-precipitation patterns, which will likely affect soil microbial communities and their functions, ultimately shifting microbially-mediated biogeochemical cycles. The present study aims to investigate the simultaneous variation of microbial community compositions and functions in response to drought and following rewetting events, using a soil metaproteomics approach. For this, an established field experiment located in an Austrian forest with two levels (moderate and severe stress) of precipitation manipulation was evaluated. The results showed that fungi were more strongly influenced by drying and rewetting (DRW) than bacteria, and that there was a drastic shift in the fungal community towards a more Ascomycota-dominated community. In terms of functional responses, a larger number of proteins and a higher functional diversity were observed in both moderate and severe DRW treatments compared to the control. Furthermore, in both DRW treatments a rise in proteins assigned to "translation, ribosomal structure, and biogenesis" and "protein synthesis" suggests a boost in microbial cell growth after rewetting. We also found that the changes within intracellular functions were associated to specific phyla, indicating that responses of microbial communities to DRW primarily shifted microbial functions. Microbial communities seem to respond to different levels of DRW stress by changing their functional potential, which may feed back to biogeochemical cycles.
Collapse
Affiliation(s)
- Dong Liu
- Institute of Soil Research, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), Peter Jordan-Straße 82, 1190 Vienna, Austria.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Katharina M Keiblinger
- Institute of Soil Research, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), Peter Jordan-Straße 82, 1190 Vienna, Austria.
| | - Sonja Leitner
- Institute of Soil Research, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), Peter Jordan-Straße 82, 1190 Vienna, Austria.
- International Livestock Research Institute (ILRI), Mazingira Centre for Environmental Research and Education, Box 30709, Nairobi 00100, Kenya.
| | - Uwe Wegner
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Straße 15, 17489 Greifswald, Germany.
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correnstraße 3, 06466, Gatersleben, Germany.
| | - Michael Zimmermann
- Institute of Soil Research, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), Peter Jordan-Straße 82, 1190 Vienna, Austria.
- Swiss Federal Office for Agriculture, Mattenhofstrasse 5, 3007 Bern, Switzerland.
| | - Stephan Fuchs
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Straße 15, 17489 Greifswald, Germany.
| | - Christian Lassek
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Straße 15, 17489 Greifswald, Germany.
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Friedrich-Ludwig-Jahn-Straße 15, 17489 Greifswald, Germany.
| | - Sophie Zechmeister-Boltenstern
- Institute of Soil Research, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), Peter Jordan-Straße 82, 1190 Vienna, Austria.
| |
Collapse
|
38
|
Bioindicators and nutrient availability through whole soil profile under orange groves after long-term different organic fertilizations. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-0479-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
39
|
Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics. J Proteomics 2019; 198:50-58. [DOI: 10.1016/j.jprot.2018.11.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023]
|
40
|
Gravuer K, Gennet S, Throop HL. Organic amendment additions to rangelands: A meta-analysis of multiple ecosystem outcomes. GLOBAL CHANGE BIOLOGY 2019; 25:1152-1170. [PMID: 30604474 PMCID: PMC6849820 DOI: 10.1111/gcb.14535] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/03/2018] [Accepted: 11/01/2018] [Indexed: 05/06/2023]
Abstract
Interest in land application of organic amendments-such as biosolids, composts, and manures-is growing due to their potential to increase soil carbon and help mitigate climate change, as well as to support soil health and regenerative agriculture. While organic amendments are predominantly applied to croplands, their application is increasingly proposed on relatively arid rangelands that do not typically receive fertilizers or other inputs, creating unique concerns for outcomes such as native plant diversity and water quality. To maximize environmental benefits and minimize potential harms, we must understand how soil, water, and plant communities respond to particular amendments and site conditions. We conducted a global meta-analysis of 92 studies in which organic amendments had been added to arid, semiarid, or Mediterranean rangelands. We found that organic amendments, on average, provide some environmental benefits (increased soil carbon, soil water holding capacity, aboveground net primary productivity, and plant tissue nitrogen; decreased runoff quantity), as well as some environmental harms (increased concentrations of soil lead, runoff nitrate, and runoff phosphorus; increased soil CO2 emissions). Published data were inadequate to fully assess impacts to native plant communities. In our models, adding higher amounts of amendment benefitted four outcomes and harmed two outcomes, whereas adding amendments with higher nitrogen concentrations benefitted two outcomes and harmed four outcomes. This suggests that trade-offs among outcomes are inevitable; however, applying low-N amendments was consistent with both maximizing benefits and minimizing harms. Short study time frames (median 1-2 years), limited geographic scope, and, for some outcomes, few published studies limit longer-term inferences from these models. Nevertheless, they provide a starting point to develop site-specific amendment application strategies aimed toward realizing the potential of this practice to contribute to climate change mitigation while minimizing negative impacts on other environmental goals.
Collapse
Affiliation(s)
- Kelly Gravuer
- Center for Biodiversity OutcomesArizona State UniversityTempeArizona
- The Nature ConservancyArlingtonVirginia
| | | | - Heather L. Throop
- School of Earth and Space ExplorationArizona State UniversityTempeArizona
- School of Life SciencesArizona State UniversityTempeArizona
| |
Collapse
|
41
|
Marín-Benito JM, Carpio MJ, Sánchez-Martín MJ, Rodríguez-Cruz MS. Previous degradation study of two herbicides to simulate their fate in a sandy loam soil: Effect of the temperature and the organic amendments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:1301-1310. [PMID: 30759570 DOI: 10.1016/j.scitotenv.2018.11.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/09/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
A laboratory study was designed to assess the following: i) the degradation kinetics of chlorotoluron and flufenacet at two different temperatures, 6 °C and 16 °C, in an unamended agricultural soil and one amended with spent mushroom substrate (SMS) and green compost (GC), and ii) the formation of the main metabolites of both herbicides with potential risk for water pollution over degradation time. The aim was to determine the dependence of these herbicide degradations on temperature (Q10 factor) using kinetic parameters, which is essential information for the later simulation of herbicide environmental fate with FOCUS models. SMS and GC were applied in situ to the natural soil as organic amendments at rates of 140 or 85 t residue ha-1, respectively. Unamended and amended soils were taken from the 0-10 cm topsoil of experimental plots (three replicates/treatment) located on an agricultural farm. Samples of soil + herbicides were incubated at 6 °C or 16 °C under laboratory conditions. The degradation curves of chlorotoluron and flufenacet were fitted to single first-order and first-order multicompartment kinetic models, respectively. The flufenacet degradation, the more hydrophobic herbicide, was slower than that of chlorotoluron in all the treatments. The application of the organic amendments to soil increased the half-lives (DT50) for both herbicides incubated at 6 °C (1.3-1.9 times) and 16 °C (1.4-1.9 times) due to their higher sorption and lower bioavailability for degradation in amended soils. The herbicides recorded a faster degradation at 16 °C than at 6 °C (Q10 = 1.9-2.8) due to the increased microbial biomass and/or activity with temperature. The metabolites desmethyl chlorotoluron, flufenacet ESA and flufenacet OA were detected in all the soil treatments at both incubation temperatures. The determination of Q10 factors in amended soils is very valuable for generating accurate input data for pesticide fate models such as FOCUS in order to improve the evaluation of the leaching of herbicides and their transformation products, which is a relevant goal to maintain the sustainability of agricultural systems.
Collapse
Affiliation(s)
- Jesús M Marín-Benito
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Cordel de Merinas 40-52, 37008 Salamanca, Spain.
| | - M José Carpio
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - María J Sánchez-Martín
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - M Sonia Rodríguez-Cruz
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Cordel de Merinas 40-52, 37008 Salamanca, Spain
| |
Collapse
|
42
|
García-Delgado C, Barba-Vicente V, Marín-Benito JM, Mariano Igual J, Sánchez-Martín MJ, Sonia Rodríguez-Cruz M. Influence of different agricultural management practices on soil microbial community over dissipation time of two herbicides. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 646:1478-1488. [PMID: 30235633 DOI: 10.1016/j.scitotenv.2018.07.395] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/20/2018] [Accepted: 07/27/2018] [Indexed: 06/08/2023]
Abstract
Soil microbiology could be affected by the presence of pesticide residues during intensive farming, potentially threatening the soil environment. The aim here was to assess the dissipation of the herbicides triasulfuron and prosulfocarb, applied as a combined commercial formulation, and the changes in soil microbial communities (through the profile of phospholipid fatty acids (PLFAs) extracted from the soil) during the dissipation time of the herbicides under field conditions. The dissipation of herbicides and the soil microbial structure were assessed under different agricultural practices, such as the repeated application of herbicides (twice), in unamended and amended soils with two organic amendments derived from green compost (GC1 and GC2) and with non-irrigation and irrigation regimes. The results obtained indicate slower dissipation for triasulfuron than for prosulfocarb. The 50% dissipation time (DT50) decreased under all conditions for the second application of triasulfuron, although not for prosulfocarb. The DT50 values for both herbicides increased in the GC2 amended soil with the highest organic carbon (OC) content. The DT50 values decreased for prosulfocarb with irrigation, but not for triasulfuron, despite its higher water solubility. The herbicides did not have any significant effects on the relative population of Gram-negative and Gram-positive bacteria during the assay, but the relative abundance of Actinobacteria increased in all the soils with herbicides. At the end of the assay (215 days), the negative effects of herbicides on fungi abundance were significant (p < 0.05) for all the treatments. These microbiological changes were detected in non-irrigated and irrigated soils, and were more noticeable after the second application of herbicides. Actinobacteria could be responsible for the modification of herbicide degradation rates, which tend to be faster after the second application. This study makes a useful contribution to the evaluation of the soil environment and microbiological risks due to the long-term repeated application of herbicides under different agricultural management practices.
Collapse
Affiliation(s)
- Carlos García-Delgado
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 40-52 Cordel de Merinas, 37008 Salamanca, Spain
| | - Víctor Barba-Vicente
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 40-52 Cordel de Merinas, 37008 Salamanca, Spain
| | - Jesús M Marín-Benito
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 40-52 Cordel de Merinas, 37008 Salamanca, Spain
| | - J Mariano Igual
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 40-52 Cordel de Merinas, 37008 Salamanca, Spain
| | - María J Sánchez-Martín
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 40-52 Cordel de Merinas, 37008 Salamanca, Spain
| | - M Sonia Rodríguez-Cruz
- Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), 40-52 Cordel de Merinas, 37008 Salamanca, Spain.
| |
Collapse
|
43
|
Gómez-Sagasti MT, Hernández A, Artetxe U, Garbisu C, Becerril JM. How Valuable Are Organic Amendments as Tools for the Phytomanagement of Degraded Soils? The Knowns, Known Unknowns, and Unknowns. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00068] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
|
44
|
Marín-Benito JM, Barba V, Ordax JM, Sánchez-Martín MJ, Rodríguez-Cruz MS. Recycling organic residues in soils as amendments: Effect on the mobility of two herbicides under different management practices. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 224:172-181. [PMID: 30041096 DOI: 10.1016/j.jenvman.2018.07.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/11/2018] [Accepted: 07/14/2018] [Indexed: 06/08/2023]
Abstract
The addition of organic residues to soil to increase its organic matter content is considered as a viable option for sustainable food production in soils sensitive to degradation and erosion. However, the recycling of these organic residues in agricultural soils needs to be previously appraised because they can modify the behaviour of pesticides when they are simultaneously applied in agricultural practices. This study evaluated the changes in the mobility and persistence of two herbicides, triasulfuron and prosulfocarb, after two repeated applications in field experimental plots in an unamended soil and one amended with green compost (GC) for seven months. Different factors were studied: i) soil without amendment (S), ii) soil amended with two doses of GC (∼12 t C ha-1, S + GC1 and 40 t C ha-1, S + GC2), and iii) soils unamended and amended with different irrigation conditions: non-irrigated and with additional irrigation (2.8 mm per week). After the first application of herbicides, the results initially indicated no significant effects of soil treatments or irrigation conditions for triasulfuron mobility in agreement with the residual concentrations in the soil profile. The effect of irrigation was noted after one month of herbicide application and the effect of the soil treatment was significant after two months because the persistence of triasulfuron in S + GC2 was maintained until 50% of the applied amount. For prosulfocarb, the influence of soil amendment was significant for the initial persistence of the herbicide in S + GC2, higher than in S or S + GC1, in agreement with its adsorption constants for this soil. However, dissipation or leaching of the herbicide over time was not inhibited in this soil. After the repeated application of herbicides, the influence of the treatment of soils and/or irrigation was significant for the leaching and dissipation of both herbicides. The initial dissipation/degradation or leaching of herbicides was higher than after the first application, although persistence was maintained after five months of application in amended soils for triasulfuron and in unamended and amended soils for prosulfocarb. The results confirm that high doses of GC increased the persistence of both herbicides. This practice may offer the possibility of applying a tailored dose of GC to soil for striking a balance between residual concentrations and the soil agronomic effect.
Collapse
Affiliation(s)
- J M Marín-Benito
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), C/ Cordel de Merinas 40-52, 37008 Salamanca, Spain.
| | - V Barba
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), C/ Cordel de Merinas 40-52, 37008 Salamanca, Spain.
| | - J M Ordax
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), C/ Cordel de Merinas 40-52, 37008 Salamanca, Spain.
| | - M J Sánchez-Martín
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), C/ Cordel de Merinas 40-52, 37008 Salamanca, Spain.
| | - M S Rodríguez-Cruz
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), C/ Cordel de Merinas 40-52, 37008 Salamanca, Spain.
| |
Collapse
|
45
|
Variation in the Soil Microbial Community of Reclaimed Land over Different Reclamation Periods. SUSTAINABILITY 2018. [DOI: 10.3390/su10072286] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
46
|
Kneller T, Harris RJ, Bateman A, Muñoz-Rojas M. Native-plant amendments and topsoil addition enhance soil function in post-mining arid grasslands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 621:744-752. [PMID: 29197793 DOI: 10.1016/j.scitotenv.2017.11.219] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/19/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
One of the most critical challenges faced in restoration of disturbed arid lands is the limited availability of topsoil. In post-mining restoration, alternative soil substrates such as mine waste could be an adequate growth media to alleviate the topsoil deficit, but these materials often lack appropriate soil characteristics to support the development and survival of seedlings. Thus, addition of exogenous organic matter may be essential to enhance plant survival and soil function. Here, we present a case study in the arid Pilbara region (north-west Western Australia), a resource-rich area subject to intensive mining activities. The main objective of our study was to assess the effects of different restoration techniques such as soil reconstruction by blending available soil materials, sowing different compositions of plant species, and addition of a locally abundant native soil organic amendment (Triodia pungens biomass) on: (i) seedling recruitment and growth of Triodia wiseana, a dominant grass in Australian arid ecosystems, and (ii) soil chemical, physical, and biological characteristics of reconstructed soils, including microbial activity, total organic C, total N, and C and N mineralisation. The study was conducted in a 12-month multifactorial microcosms setting in a controlled environment. Our results showed that the amendment increased C and N contents of re-made soils, but these values were still lower than those obtained in the topsoil. High microbial activity and C mineralisation rates were found in the amended waste that contrasted the low N mineralisation but this did not translate into improved emergence or survival of T. wiseana. These results suggest a short- or medium-term soil N immobilisation caused by negative priming effect of fresh un-composted amendment on microbial communities. We found similar growth and survival rates of T. wiseana in topsoil and a blend of topsoil and waste (50:50) which highlights the importance of topsoil, even in a reduced amount, for plant establishment in arid land restoration.
Collapse
Affiliation(s)
- Tayla Kneller
- Kings Park and Botanic Garden, Kings Park 6005, WA, Australia; Curtin University, Department of Environment and Agriculture, Bentley 6102, WA, Australia
| | - Richard J Harris
- Curtin University, Department of Environment and Agriculture, Bentley 6102, WA, Australia
| | - Amber Bateman
- Kings Park and Botanic Garden, Kings Park 6005, WA, Australia; University of Western Australia, School of Biological Sciences, Crawley 6009, WA, Australia
| | - Miriam Muñoz-Rojas
- Kings Park and Botanic Garden, Kings Park 6005, WA, Australia; University of Western Australia, School of Biological Sciences, Crawley 6009, WA, Australia; University of New South Wales, School of Biological, Earth and Environmental Sciences, Randwick 2052, NSW, Australia.
| |
Collapse
|
47
|
Bastida F, Jehmlich N, Torres IF, García C. The extracellular metaproteome of soils under semiarid climate: A methodological comparison of extraction buffers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 619-620:707-711. [PMID: 29156289 DOI: 10.1016/j.scitotenv.2017.11.134] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/24/2017] [Accepted: 11/12/2017] [Indexed: 06/07/2023]
Abstract
We compare the protein extraction efficiencies, as well as the phylogenetic and functional information provided, of two extraction protocols in soils that differ mainly in their organic matter and clay contents, the main factors limiting protein extraction in semiarid soils. These protocols utilise extractants commonly used for the assay of extracellular enzyme activities. The first method was based on the utilisation of the modified universal buffer (MUB). The second was based on the extraction of humic substances with sodium pyrophosphate. When compared to the total amount of proteins in soil, the results indicate a very-low extraction efficiency for both protocols. Analysis in an Orbitrap Fusion mass spectrometer and further searching against an "ad hoc" metagenome evidenced that the phylogenetic and functional information retrieved from the extracellular soil metaproteome can be biased by the extraction buffer.
Collapse
Affiliation(s)
- F Bastida
- CEBAS-CSIC, Department of Soil and Water Conservation, campus Universitario de Espinardo, 30100 Murcia, Spain.
| | - N Jehmlich
- Helmholtz-Centre for Environmental Research, UFZ, Department of Molecular Systems Biology, Permoserstr. 15, 04318 Leipzig, Germany
| | - I F Torres
- CEBAS-CSIC, Department of Soil and Water Conservation, campus Universitario de Espinardo, 30100 Murcia, Spain
| | - C García
- CEBAS-CSIC, Department of Soil and Water Conservation, campus Universitario de Espinardo, 30100 Murcia, Spain
| |
Collapse
|
48
|
Bai Z, Xie H, Kao-Kniffin J, Chen B, Shao P, Liang C. Shifts in microbial trophic strategy explain different temperature sensitivity of CO2 flux under constant and diurnally varying temperature regimes. FEMS Microbiol Ecol 2017; 93:3814241. [PMID: 28499007 DOI: 10.1093/femsec/fix063] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/09/2017] [Indexed: 12/31/2022] Open
Abstract
Understanding soil CO2 flux temperature sensitivity (Q10) is critical for predicting ecosystem-level responses to climate change. Yet, the effects of warming on microbial CO2 respiration still remain poorly understood under current Earth system models, partly as a result of thermal acclimation of organic matter decomposition. We conducted a 117-day incubation experiment under constant and diurnally varying temperature treatments based on four forest soils varying in vegetation stand and soil horizon. Our results showed that Q10 was greater under varying than constant temperature regimes. This distinction was most likely attributed to differences in the depletion of available carbon between constant high and varying high-temperature treatments, resulting in significantly higher rates of heterotrophic respiration in the varying high-temperature regime. Based on 16S rRNA gene sequencing data using Illumina, the varying high-temperature regime harbored higher prokaryotic alpha-diversity, was more dominated by the copiotrophic strategists and sustained a distinct community composition, in comparison to the constant-high treatment. We found a tightly coupled relationship between Q10 and microbial trophic guilds: the copiotrophic prokaryotes responded positively with high Q10 values, while the oligotrophs showed a negative response. Effects of vegetation stand and soil horizon consistently supported that the copiotrophic vs oligotrophic strategists determine the thermal sensitivity of CO2 flux. Our observations suggest that incorporating prokaryotic functional traits, such as shifts between copiotrophy and oligotrophy, is fundamental to our understanding of thermal acclimation of microbially mediated soil organic carbon cycling. Inclusion of microbial functional shifts may provide the potential to improve our projections of responses in microbial community and CO2 efflux to a changing environment in forest ecosystems.
Collapse
Affiliation(s)
- Zhen Bai
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Hongtu Xie
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Jenny Kao-Kniffin
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengshuai Shao
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| |
Collapse
|
49
|
Bai Z, Ma Q, Dai Y, Yuan H, Ye J, Yu W. Spatial Heterogeneity of SOM Concentrations Associated with White-rot Versus Brown-rot Wood Decay. Sci Rep 2017; 7:13758. [PMID: 29062128 PMCID: PMC5653805 DOI: 10.1038/s41598-017-14181-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/05/2017] [Indexed: 11/08/2022] Open
Abstract
White- and brown-rot fungal decay via distinct pathways imparts characteristic molecular imprints on decomposing wood. However, the effect that a specific wood-rotting type of fungus has on proximal soil organic matter (SOM) accumulation remains unexplored. We investigated the potential influence of white- and brown-rot fungi-decayed Abies nephrolepis logs on forest SOM stocks (i.e., soil total carbon (C) and nitrogen (N)) and the concentrations of amino sugars (microbial necromass) at different depths and horizontal distances from decaying woody debris. The brown-rot fungal wood decay resulted in higher concentrations of soil C and N and a greater increase in microbial necromass (i.e., 1.3- to 1.7-fold greater) than the white-rot fungal wood decay. The white-rot sets were accompanied by significant differences in the proportions of the bacterial residue index (muramic acid%) with soil depth; however, the brown-rot-associated soils showed complementary shifts, primarily in fungal necromass, across horizontal distances. Soil C and N concentrations were significantly correlated with fungal rather than bacterial necromass in the brown-rot systems. Our findings confirmed that the brown-rot fungi-dominated degradation of lignocellulosic residues resulted in a greater SOM buildup than the white-rot fungi-dominated degradation.
Collapse
Affiliation(s)
- Zhen Bai
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Qiang Ma
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China.
| | - Yucheng Dai
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Haisheng Yuan
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Ji Ye
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Wantai Yu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China.
| |
Collapse
|
50
|
Bastida F, Torres IF, Andrés-Abellán M, Baldrian P, López-Mondéjar R, Větrovský T, Richnow HH, Starke R, Ondoño S, García C, López-Serrano FR, Jehmlich N. Differential sensitivity of total and active soil microbial communities to drought and forest management. GLOBAL CHANGE BIOLOGY 2017; 23:4185-4203. [PMID: 28614633 DOI: 10.1111/gcb.13790] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/30/2017] [Indexed: 05/25/2023]
Abstract
Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning-that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 6 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community-based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought-plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial community and climate change.
Collapse
Affiliation(s)
- Felipe Bastida
- Department of Soil and Water Conservation, CEBAS-CSIC, Murcia, Spain
| | - Irene F Torres
- Department of Soil and Water Conservation, CEBAS-CSIC, Murcia, Spain
| | - Manuela Andrés-Abellán
- Department of Science and Agroforestry Technology and Genetics, Higher Technical School of Agricultural and Forestry Engineering, University of Castilla-La Mancha, Albacete, Spain
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Praha 4, Czech Republic
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Robert Starke
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sara Ondoño
- Department of Soil and Water Conservation, CEBAS-CSIC, Murcia, Spain
| | - Carlos García
- Department of Soil and Water Conservation, CEBAS-CSIC, Murcia, Spain
| | - Francisco R López-Serrano
- Department of Science and Agroforestry Technology and Genetics, Higher Technical School of Agricultural and Forestry Engineering, University of Castilla-La Mancha, Albacete, Spain
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| |
Collapse
|