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Tomazelli D, Klauberg-Filho O, Mendes LW, Goss-Souza D. The impact of land-use changes and management intensification on bacterial communities in the last decade: a review. Appl Environ Microbiol 2024; 90:e0030924. [PMID: 38874336 PMCID: PMC11267915 DOI: 10.1128/aem.00309-24] [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] [Indexed: 06/15/2024] Open
Abstract
In the last decade, advances in soil bacterial ecology have contributed to increasing agricultural production. Brazil is the world leading agriculture producer and leading soil biodiversity reservoir. Meanwhile, there is still a significant gap in the knowledge regarding the soil microscopic life and its interactions with agricultural practices, and the replacement of natural vegetation by agroecosystems is yet to be unfolded. Through high throughput DNA sequencing, scientists are now exploring the complexity of soil bacterial communities and their relationship with soil and environmental characteristics. This study aimed to investigate the progress of bacterial ecology studies in Brazil over the last 10 years, seeking to understand the effect of the conversion of natural vegetation in agricultural systems on the diversity and structure of the soil microbial communities. We conducted a systematic search for scientific publication databases. Our systematic search has matched 62 scientific articles from three different databases. Most of the studies were placed in southeastern and northern Brazil, with no records of studies about microbial ecology in 17 out of 27 Brazilian states. Out of the 26 studies that examined the effects of replacing natural vegetation with agroecosystems, most authors concluded that changes in soil pH and vegetation cover replacement were the primary drivers of shifts in microbial communities. Understanding the ecology of the bacteria inhabiting Brazilian soils in agroecosystems is paramount for developing more efficient soil management strategies and cleaner agricultural technologies.
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Affiliation(s)
- Daniela Tomazelli
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, Santa Catarina, Brazil
| | - Osmar Klauberg-Filho
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, Santa Catarina, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Dennis Goss-Souza
- College of Agronomy, Federal Institute of Paraná, Palmas, Paraná, Brazil
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Gangwar RK, Táncsics A, Makádi M, Farkas M, Cserháti M, Michéli E, Fuchs M, Szegi T. Bacterial community composition of Hungarian salt-affected soils under different land uses. Biol Futur 2024:10.1007/s42977-024-00235-1. [PMID: 39030426 DOI: 10.1007/s42977-024-00235-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
Abstract
Salinization and sodification are serious and worldwide growing threats to healthy soil functions. Although plants developed a plethora of traits to cope with high salinity, soil bacteria are also essential players of the adaptation process. However, there is still lack of knowledge on how other biotic and abiotic factors, such as land use or different soil properties, affect the bacterial community structure of these soils. Therefore, besides soil chemical and physical investigations, bacterial communities of differently managed salt-affected soils were analysed through 16S rRNA gene Illumina amplicon sequencing and compared. Results have shown that land use and soil texture were the main drivers in shaping the bacterial community structure of the Hungarian salt-affected soils. It was observed that at undisturbed pasture and meadow sites, soil texture and the ratio of vegetation cover were the determinative factors shaping the bacterial community structures, mainly at the level of phylum Acidobacteriota. Sandy soil texture promoted the high abundance of members of the class Blastocatellia, while at the slightly disturbed meadow soil showing high clay content was dominated by members of the class Acidobacteriia. The OTUs belonging to the class Ktedonobacteria, which were reported mostly in geothermal sediments, reached a relatively high abundance in the meadow soil.
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Affiliation(s)
- Ravi Kumar Gangwar
- Department of Soil Science, Institute of Environmental Sciences, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary
| | - András Táncsics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary.
| | - Marianna Makádi
- Research Institute of Nyíregyháza, IAREF, University of Debrecen, Westsik Vilmos utca 4-6, Nyíregyháza, 4400, Hungary
| | - Milán Farkas
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary
| | - Mátyás Cserháti
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary
| | - Erika Michéli
- Department of Soil Science, Institute of Environmental Sciences, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary
| | - Márta Fuchs
- Department of Soil Science, Institute of Environmental Sciences, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary
| | - Tamás Szegi
- Department of Soil Science, Institute of Environmental Sciences, Hungarian University of Agriculture and Life Sciences, Páter Károly u. 1, Gödöllő, 2100, Hungary
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Fiard M, Militon C, Sylvi L, Migeot J, Michaud E, Jézéquel R, Gilbert F, Bihannic I, Devesa J, Dirberg G, Cuny P. Uncovering potential mangrove microbial bioindicators to assess urban and agricultural pressures on Martinique island in the eastern Caribbean Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172217. [PMID: 38583633 DOI: 10.1016/j.scitotenv.2024.172217] [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: 01/12/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Martinique's mangroves, which cover 1.85 ha of the island (<0.1 % of the total area), are considerably vulnerable to local urban, agricultural, and industrial pollutants. Unlike for temperate ecosystems, there are limited indicators that can be used to assess the anthropogenic pressures on mangroves. This study investigated four stations on Martinique Island, with each being subject to varying anthropogenic pressures. An analysis of mangrove sediment cores approximately 18 cm in depth revealed two primary types of pressures on Martinique mangroves: (i) an enrichment in organic matter in the two stations within the highly urbanized bay of Fort-de-France and (ii) agricultural pressure observed in the four studied mangrove stations. This pressure was characterized by contamination, exceeding the regulatory thresholds, with dieldrin, total DDT, and metals (As, Cu and Ni) found in phytosanitary products. The mangroves of Martinique are subjected to varying degrees of anthropogenic pressure, but all are subjected to contamination by organochlorine pesticides. Mangroves within the bay of Fort-de-France experience notably higher pressures compared to those in the island's northern and southern regions. In these contexts, the microbial communities exhibited distinct responses. The microbial biomass and the abundance of bacteria and archaea were higher in the two less-impacted stations, while in the mangrove of Fort-de-France, various phyla typically associated with polluted environments were more prevalent. These differences in the microbiota composition led to the identification of 65 taxa, including Acanthopleuribacteraceae, Spirochaetaceae, and Pirellulaceae, that could potentially serve as indicators of an anthropogenic influence on the mangrove sediments of Martinique Island.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Jonathan Migeot
- Impact Mer consulting, expertise, and R&D firm, 20 rue Karukéra, 97200 Fort de France, Martinique/FWI, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Ronan Jézéquel
- CEDRE, 715 rue Alain Colas, 29218 Brest CEDEX 2, France.
| | - Franck Gilbert
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier, Toulouse, France.
| | | | - Jeremy Devesa
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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Jiao F, Qian L, Wu J, Zhang D, Zhang J, Wang M, Sui X, Zhang X. Diversity and Composition of Soil Acidobacterial Communities in Different Temperate Forest Types of Northeast China. Microorganisms 2024; 12:963. [PMID: 38792792 PMCID: PMC11124458 DOI: 10.3390/microorganisms12050963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
To gain an in-depth understanding of the diversity and composition of soil Acidobacteria in five different forest types in typical temperate forest ecosystems and to explore their relationship with soil nutrients. The diversity of soil Acidobacteria was determined by high-throughput sequencing technology. Soil Acidobacteria's alpha-diversity index and soil nutrient content differed significantly among different forest types. β-diversity and the composition of soil Acidobacteria also varied across forest types. Acidobacterial genera, such as Acidobacteria_Gp1, Acidobacteria_Gp4, and Acidobacteria_Gp17, play key roles in different forests. The RDA analyses pointed out that the soil pH, available nitrogen (AN), carbon to nitrogen (C/N) ratio, available phosphorus (AP), total carbon (TC), and total phosphorus (TP) were significant factors affecting soil Acidobacteria in different forest types. In this study, the diversity and composition of soil Acidobacteria under different forest types in a temperate forest ecosystem were analyzed, revealing the complex relationship between them and soil physicochemical properties. These findings not only enhance our understanding of soil microbial ecology but also provide important guidance for ecological conservation and restoration strategies for temperate forest ecosystems.
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Affiliation(s)
- Feng Jiao
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Lili Qian
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Jinhua Wu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Dongdong Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Junying Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Xianbang Zhang
- Heilongjiang Zhongyangzhan Black-Billed Capercaillie National Nature Reserve Service Center, Nenjiang 161400, China
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Kuo J, Liu D, Wen WH, Chiu CY, Chen W, Wu YW, Lai FT, Lin CH. Different microbial communities in paddy soils under organic and nonorganic farming. Braz J Microbiol 2024; 55:777-788. [PMID: 38147271 PMCID: PMC10920611 DOI: 10.1007/s42770-023-01218-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023] Open
Abstract
Organic agriculture is a farming method that provides healthy food and is friendly to the environment, and it is developing rapidly worldwide. This study compared microbial communities in organic farming (Or) paddy fields to those in nonorganic farming (Nr) paddy fields based on 16S rDNA sequencing and analysis. The predominant microorganisms in both soils were Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, and Nitrospirota. The alpha diversity of the paddy soil microbial communities was not different between the nonorganic and organic farming systems. The beta diversity of nonmetric multidimensional scaling (NMDS) revealed that the two groups were significantly separated. Distance-based redundancy analysis (db-RDA) suggested that soil pH and electrical conductivity (EC) had a positive relationship with the microbes in organic paddy soils. There were 23 amplicon sequence variants (ASVs) that showed differential abundance. Among them, g_B1-7BS (Proteobacteria), s_Sulfuricaulis limicola (Proteobacteria), g_GAL15 (p_GAL15), c_Thermodesulfovibrionia (Nitrospirota), two of f_Anaerolineaceae (Chloroflexi), and two of g_S085 (Chloroflexi) showed that they were more abundant in organic soils, whereas g_11-24 (Acidobacteriota), g__Subgroup_7 (Acidobacteriota), and g_Bacillus (Firmicutes) showed differential abundance in nonorganic paddy soils. Functional prediction of microbial communities in paddy soils showed that functions related to carbohydrate metabolism could be the major metabolic activities. Our work indicates that organic farming differs from nonorganic farming in terms of microbial composition in paddy soils and provides specific microbes that might be helpful for understanding soil fertility.
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Affiliation(s)
- Jimmy Kuo
- Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung, 94450, Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, 94450, Taiwan
| | - Daniel Liu
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Wei Hao Wen
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Ching Yuan Chiu
- Department of Bioresources, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Wanyu Chen
- Department of Bioresources, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Yun Wen Wu
- Department of Bioresources, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Fang-Ting Lai
- Department of Medicinal Botanicals and Foods On Health Applications, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Chorng-Horng Lin
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan.
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Hou XY, Qiao WT, Gu JD, Liu CY, Hussain MM, Du DL, Zhou Y, Wang YF, Li Q. Reforestation of Cunninghamia lanceolata changes the relative abundances of important prokaryotic families in soil. Front Microbiol 2024; 15:1312286. [PMID: 38414777 PMCID: PMC10896735 DOI: 10.3389/fmicb.2024.1312286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Abstract
Over the past decades, many forests have been converted to monoculture plantations, which might affect the soil microbial communities that are responsible for governing the soil biogeochemical processes. Understanding how reforestation efforts alter soil prokaryotic microbial communities will therefore inform forest management. In this study, the prokaryotic communities were comparatively investigated in a secondary Chinese fir forest (original) and a reforested Chinese fir plantation (reforested from a secondary Chinese fir forest) in Southern China. The results showed that reforestation changed the structure of the prokaryotic community: the relative abundances of important prokaryotic families in soil. This might be caused by the altered soil pH and organic matter content after reforestation. Soil profile layer depth was an important factor as the upper layers had a higher diversity of prokaryotes than the lower ones (p < 0.05). The composition of the prokaryotic community presented a seasonality characteristic. In addition, the results showed that the dominant phylum was Acidobacteria (58.86%) with Koribacteraceae (15.38%) as the dominant family in the secondary Chinese fir forest and the reforested plantation. Furthermore, soil organic matter, total N, hydrolyzable N, and NH 4 + - N were positively correlated with prokaryotic diversity (p < 0.05). Also, organic matter and NO 3 - - N were positively correlated to prokaryotic abundance (p < 0.05). This study demonstrated that re-forest transformation altered soil properties, which lead to the changes in microbial composition. The changes in microbial community might in turn influence biogeochemical processes and the environmental variables. The study could contribute to forest management and policy-making.
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Affiliation(s)
- Xue-Yan Hou
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Wen-Tao Qiao
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion Israel Institute of Technology, Shantou, China
| | - Chao-Ying Liu
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Muhammad Mahroz Hussain
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Dao-Lin Du
- Jingjiang College, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Yi Zhou
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Yong-Feng Wang
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Qian Li
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
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Faghihinia M, Halverson LJ, Hršelová H, Bukovská P, Rozmoš M, Kotianová M, Jansa J. Nutrient-dependent cross-kingdom interactions in the hyphosphere of an arbuscular mycorrhizal fungus. Front Microbiol 2024; 14:1284648. [PMID: 38239731 PMCID: PMC10794670 DOI: 10.3389/fmicb.2023.1284648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction The hyphosphere of arbuscular mycorrhizal (AM) fungi is teeming with microbial life. Yet, the influence of nutrient availability or nutrient forms on the hyphosphere microbiomes is still poorly understood. Methods Here, we examined how the microbial community (prokaryotic, fungal, protistan) was affected by the presence of the AM fungus Rhizophagus irregularis in the rhizosphere and the root-free zone, and how different nitrogen (N) and phosphorus (P) supplements into the root-free compartment influenced the communities. Results The presence of AM fungus greatly affected microbial communities both in the rhizosphere and the root-free zone, with prokaryotic communities being affected the most. Protists were the only group of microbes whose richness and diversity were significantly reduced by the presence of the AM fungus. Our results showed that the type of nutrients AM fungi encounter in localized patches modulate the structure of hyphosphere microbial communities. In contrast we did not observe any effects of the AM fungus on (non-mycorrhizal) fungal community composition. Compared to the non-mycorrhizal control, the root-free zone with the AM fungus (i.e., the AM fungal hyphosphere) was enriched with Alphaproteobacteria, some micropredatory and copiotroph bacterial taxa (e.g., Xanthomonadaceae and Bacteroidota), and the poorly characterized and not yet cultured Acidobacteriota subgroup GP17, especially when phytate was added. Ammonia-oxidizing Nitrosomonas and nitrite-oxidizing Nitrospira were significantly suppressed in the presence of the AM fungus in the root-free compartment, especially upon addition of inorganic N. Co-occurrence network analyses revealed that microbial communities in the root-free compartment were complex and interconnected with more keystone species when AM fungus was present, especially when the root-free compartment was amended with phytate. Conclusion Our study showed that the form of nutrients is an important driver of prokaryotic and eukaryotic community assembly in the AM fungal hyphosphere, despite the assumed presence of a stable and specific AM fungal hyphoplane microbiome. Predictable responses of specific microbial taxa will open the possibility of using them as co-inoculants with AM fungi, e.g., to improve crop performance.
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Affiliation(s)
- Maede Faghihinia
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, United States
| | - Larry J. Halverson
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, United States
| | - Hana Hršelová
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Petra Bukovská
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Martin Rozmoš
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Michala Kotianová
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Jan Jansa
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
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Coluccia M, Besaury L. Acidobacteria members harbour an abundant and diverse carbohydrate-active enzymes (cazyme) and secreted proteasome repertoire, key factors for potential efficient biomass degradation. Mol Genet Genomics 2023:10.1007/s00438-023-02045-x. [PMID: 37335345 DOI: 10.1007/s00438-023-02045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
The Acidobacteria phylum is a very abundant group (20-30% of microbial communities in soil ecosystems); however, little is known about these microorganisms and their ability to degrade the biomass and lignocellulose due to the difficulty of culturing them. We, therefore, bioinformatically studied the content of lignocellulolytic enzymes (total and predicted secreted enzymes) and secreted peptidases in an in silico library containing 41 Acidobacteria genomes. The results showed a high abundance and diversity of total and secreted Carbohydrate-Active enzymes (cazyme) families among the Acidobacteria compared to known previous degraders. Indeed, the relative abundance of cazymes in some genomes represented more than 6% of the gene coding proteins with at least 300 cazymes. The same observation was made with the predicted secreted peptidases with several families of secreted peptidases, which represented at least 1.5% of the gene coding proteins in several genomes. These results allowed us to highlight the lignocellulolytic potential of the Acidobacteria phylum in the degradation of lignocellulosic biomass, which could explain its high abundance in the environment.
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Affiliation(s)
- Marion Coluccia
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
| | - Ludovic Besaury
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
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Lee J, Zhou X, Seo YO, Lee ST, Yun J, Yang Y, Kim J, Kang H. Effects of vegetation shift from needleleaf to broadleaf species on forest soil CO 2 emission. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158907. [PMID: 36150592 DOI: 10.1016/j.scitotenv.2022.158907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Forest soil harbors diverse microbial communities with decisive roles in ecosystem processes. Vegetation shift from needleleaf to broadleaf species is occurring across the globe due to climate change and anthropogenic activities, potentially change forest soil microbial communities and C cycle. However, our knowledge on the impact of such vegetation shift on soil microbial community and activities, and its consequences on forest soil C dynamics are still not well established. Here, we examined the seasonal variation of soil CO2 emission, soil extracellular enzyme activities (EEAs), and soil bacterial, fungal communities in subtropical forest from broadleaf, needleleaf, and mixed stands. In addition, soil CO2 emission and soil EEAs were measured in temperate forest during the growing season. Soil organic matter (SOM) content significantly differs between broadleaf and needleleaf forests and primarily distinguish various soil chemical and microbial characteristics. Significantly higher EEAs and soil CO2 emission in broadleaf forest compared to needleleaf forest were observed both in subtropical and temperate forests. The relative abundance of Basidiomycota positively correlated with SOM and EEAs and indirectly increase soil CO2 emission whereas the relative abundance of Ascomycota exhibits opposite trend, suggesting that soil fungal communities play a key role in determining the different microbial activities between broadleaf and needleleaf stands. The temperature sensitivity of soil CO2 emission was significantly higher in broadleaf forest compared to needleleaf forest, further suggesting that the soil organic carbon in broadleaf forests is more vulnerable to warming.
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Affiliation(s)
- Jaehyun Lee
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea; Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - Xue Zhou
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea; College of Agricultural Science and Engineering, Hohai University, China
| | - Yeon Ok Seo
- Warm Temperate and Subtropical Forest Research Center, National Institute of Forest Science, Republic of Korea
| | - Sang Tae Lee
- Lab of Silvicultural Practices and Management, National Institute of Forest Science, Republic of Korea
| | - Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea
| | - Yerang Yang
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea
| | - Jinhyun Kim
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea.
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Sui X, Frey B, Yang L, Liu Y, Zhang R, Ni H, Li MH. Soil Acidobacterial community composition changes sensitively with wetland degradation in northeastern of China. Front Microbiol 2022; 13:1052161. [PMID: 36620014 PMCID: PMC9816132 DOI: 10.3389/fmicb.2022.1052161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Acidobacteria are a major component of the soil bacteria and are conducted for many soil functions, and the soil Acidobacterial structure and diversity are affected by climate changes and human activities. However, soil Acidobacterial structure and diversity in wetland ecosystems are still limited recognized. The current study aimed to study the Acidobacterial community and diversity in relation to soil environmental factors along a typical degradation series from primitive wetland to forest in a representative fresh wetland in northeastern China. In this research, we assessed the soil Acidobacterial community composition, using Illumina MiSeq sequencing along a typical degradation series from primitive wetland to forest in a representative fresh wetland in northeastern China. The soil physico chemical properties changed significantly among the eight degrade stages (p < 0.05). The α diversity index (Shannon and Chao1 index) of soil Acidobacteria changed significantly between different degradation stages (p < 0.05). Principal Coordinates Analysis (PCoA) revealed that the soil acidobacteiral communities obviously separated into wetland group and forest group. The most abundant subgroups of Acidobacteria accounted for 31% (Gp1), 5% (Gp2), 12% (Gp3), 2% (Gp4), 5% (Gp6), and 2% (Gp7) in soils within eight successional series. The compositions of soil Acidobacteria in wetland stages were significantly affected by soil moisture content, soil total nitrogen and available nitrogen contents, while those in forest stages were significantly driven by soil pH, soil organic carbon, total nitrogen, available phosphorus and soil moisture content. Our results indicated that the soil Acidobacterial community was mainly structured by soil physico chemical parameters, and wetland degradation towards forests will greatly influence the soil Acidobacterial structure and thus the wetland functions.
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Affiliation(s)
- Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
- Snow and Landscape Research WSLSwiss Federal Institute for Forest, , Birmensdorf, Switzerland
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Beat Frey
- Snow and Landscape Research WSLSwiss Federal Institute for Forest, , Birmensdorf, Switzerland
| | - Libin Yang
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Yingnan Liu
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Rongtao Zhang
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Hongwei Ni
- Heilongjiang Academy of Forestry, Harbin, China
| | - Mai-He Li
- Snow and Landscape Research WSLSwiss Federal Institute for Forest, , Birmensdorf, Switzerland
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
- School of Life Science, Hebei University, Baoding, China
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11
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Palomo A, Dechesne A, Pedersen AG, Smets BF. Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira. MICROBIOME 2022; 10:204. [PMID: 36451244 PMCID: PMC9714041 DOI: 10.1186/s40168-022-01411-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/03/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND The discovery of microorganisms capable of complete ammonia oxidation to nitrate (comammox) has prompted a paradigm shift in our understanding of nitrification, an essential process in N cycling, hitherto considered to require both ammonia oxidizing and nitrite oxidizing microorganisms. This intriguing metabolism is unique to the genus Nitrospira, a diverse taxon previously known to only contain canonical nitrite oxidizers. Comammox Nitrospira have been detected in diverse environments; however, a global view of the distribution, abundance, and diversity of Nitrospira species is still incomplete. RESULTS In this study, we retrieved 55 metagenome-assembled Nitrospira genomes (MAGs) from newly obtained and publicly available metagenomes. Combined with publicly available MAGs, this constitutes the largest Nitrospira genome database to date with 205 MAGs, representing 132 putative species, most without cultivated representatives. Mapping of metagenomic sequencing reads from various environments against this database enabled an analysis of the distribution and habitat preferences of Nitrospira species. Comammox Nitrospira's ecological success is evident as they outnumber and present higher species-level richness than canonical Nitrospira in all environments examined, except for marine and wastewaters samples. The type of environment governs Nitrospira species distribution, without large-scale biogeographical signal. We found that closely related Nitrospira species tend to occupy the same habitats, and that this phylogenetic signal in habitat preference is stronger for canonical Nitrospira species. Comammox Nitrospira eco-evolutionary history is more complex, with subclades achieving rapid niche divergence via horizontal transfer of genes, including the gene encoding hydroxylamine oxidoreductase, a key enzyme in nitrification. CONCLUSIONS Our study expands the genomic inventory of the Nitrospira genus, exposes the ecological success of complete ammonia oxidizers within a wide range of habitats, identifies the habitat preferences of (sub)lineages of canonical and comammox Nitrospira species, and proposes that horizontal transfer of genes involved in nitrification is linked to niche separation within a sublineage of comammox Nitrospira. Video Abstract.
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Affiliation(s)
- Alejandro Palomo
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Arnaud Dechesne
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Anders G. Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Barth F. Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
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12
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Santofimia E, González FJ, Rincón-Tomás B, López-Pamo E, Marino E, Reyes J, Bellido E. The mobility of thorium, uranium and rare earth elements from Mid Ordovician black shales to acid waters and its removal by goethite and schwertmannite. CHEMOSPHERE 2022; 307:135907. [PMID: 35932924 DOI: 10.1016/j.chemosphere.2022.135907] [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: 06/07/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Previous studies have addressed the occurrence of Acid Rock Drainage (ARD) affecting La Silva stream due to the generation of large dumps of Middle Ordovician black shales during the construction of a highway close to El Bierzo (León, Spain). This ARD was characterized by sulphated acid waters with high concentration of heavy metals and anomalies in dissolved thorium (Th) and uranium (U). In the present study, we analyse in depth black shales and water, streambed sediments and precipitates of La Silva stream and its tributaries using different petrographic, mineralogical and geochemical approaches. Black shales, with average Th and U contents of 20 and 3 μg/g respectively contain disseminated detritic micro-grains of high weathering-resistant minerals, such as monazite and xenotime, that present smaller amounts of yttrium and rare earth elements (REY) and other elements as Ca, U, Th, Si and F. Results of the affected waters by ARD show an enrichment in dissolved Th, U and REY of several orders of magnitude with respect to natural waters. Sampled precipitates were mainly schwertmannite (Fe8O8(OH)8-2x (SO4)xO16•nH2O) and goethite (α-Fe3+O(OH)) that showed an enrichment of Th (up to 798 μg/g) and REY, due to the presence of dissolved anionic species (e.g. [Formula: see text] , [Formula: see text] ) that enables their adsorption. Furthermore, these black shales show a clear enrichment in REE (Rare Earth Elements) with respect to NASC (North American Shales Composite) normalized REE patterns. Likewise, normalized REE patterns of stream waters and precipitates clearly show convex curvatures in middle-REE (MREE) with respect to light- and something less than heavy-REE, indicating the trend towards MREE enrichment. These findings are essential to evaluate the impact of ARD of Mid Ordovician shales in the surrounding environment, and to start considering these site as potential source of REE and critical raw materials, activating a Circular Economy.
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Affiliation(s)
- Esther Santofimia
- Instituto Geológico y Minero de España (IGME-CSIC), Ríos Rosas, 23, 28003, Madrid, Spain.
| | | | - Blanca Rincón-Tomás
- Instituto Geológico y Minero de España (IGME-CSIC), Ríos Rosas, 23, 28003, Madrid, Spain; Georg-August-University Göttingen, Grisebachstr., 8, 37077, Göttingen, Germany
| | - Enrique López-Pamo
- Instituto Geológico y Minero de España (IGME-CSIC), Ríos Rosas, 23, 28003, Madrid, Spain
| | - Egidio Marino
- Instituto Geológico y Minero de España (IGME-CSIC), Ríos Rosas, 23, 28003, Madrid, Spain
| | - Jesús Reyes
- Instituto Geológico y Minero de España (IGME-CSIC), Ríos Rosas, 23, 28003, Madrid, Spain
| | - Eva Bellido
- Instituto Geológico y Minero de España (IGME-CSIC), Ríos Rosas, 23, 28003, Madrid, Spain
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13
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Pin Viso ND, Rizzo PF, Young BJ, Gabioud E, Bres P, Riera NI, Merino L, Farber MD, Crespo DC. The Use of Raw Poultry Waste as Soil Amendment Under Field Conditions Caused a Loss of Bacterial Genetic Diversity Together with an Increment of Eutrophic Risk and Phytotoxic Effects. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02119-0. [PMID: 36197502 DOI: 10.1007/s00248-022-02119-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Poultry waste has been used as fertilizer to avoid soil degradation caused by the long-term application of chemical fertilizer. However, few studies have evaluated field conditions where livestock wastes have been used for extended periods of time. In this study, physicochemical parameters, metabarcoding of the 16S rRNA gene, and ecotoxicity indexes were used for the characterization of chicken manure and poultry litter to examine the effect of their application to agricultural soils for 10 years. Poultry wastes showed high concentrations of nutrients and increased electrical conductivity leading to phytotoxic effects on seeds. The bacterial communities were dominated by typical members of the gastrointestinal tract, noting the presence of pathogenic bacteria. Soils subjected to poultry manure applications showed statistically higher values of total and extractable phosphorous, increasing the risk of eutrophication. Moreover, while the soil bacterial community remained dominated by the ones related to the biogeochemical cycles of nutrients and plant growth promotion, losses of alpha diversity were observed on treated soils. Altogether, our work would contribute to understand the effects of common local agricultural practices and support the adoption of the waste treatment process in compliance with environmental sustainability guidelines.
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Affiliation(s)
- Natalia D Pin Viso
- Instituto de Agrobiotecnología y Biología Molecular, IABiMo, INTA-CONICET, Calle Las Cabañas y Los Reseros s/n, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina
- Universidad Nacional de Hurlingham, Tte. Origone 151, 1688, Hurlingham, Buenos Aires, Argentina
| | - Pedro F Rizzo
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Brian J Young
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Emmanuel Gabioud
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Paraná, Ruta 11 Km 12.5, 3101, Oro Verde, Entre Ríos, Argentina
| | - Patricia Bres
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Nicolás I Riera
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Lina Merino
- Universidad Nacional de Hurlingham, Tte. Origone 151, 1688, Hurlingham, Buenos Aires, Argentina
| | - Marisa D Farber
- Instituto de Agrobiotecnología y Biología Molecular, IABiMo, INTA-CONICET, Calle Las Cabañas y Los Reseros s/n, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina.
- Universidad Nacional de Hurlingham, Tte. Origone 151, 1688, Hurlingham, Buenos Aires, Argentina.
| | - Diana C Crespo
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
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14
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Bai Z, Zheng L, Bai Z, Jia A, Wang M. Long-term cultivation alter soil bacterial community in a forest-grassland transition zone. Front Microbiol 2022; 13:1001781. [PMID: 36246280 PMCID: PMC9557053 DOI: 10.3389/fmicb.2022.1001781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Changes in land use types can significantly affect soil porperties and microbial community composition in many areas. However, the underlying mechanism of shift in bacterial communities link to soil properties is still unclear. In this study, Illumina high-throughput sequencing was used to analyze the changes of soil bacterial communities in different land use types in a forest-grassland transition zone, North China. There are two different land use types: grassland (G) and cultivated land (CL). Meanwhile, cultivated land includes cultivated of 10 years (CL10) or 20 years (CL20). Compared with G, CL decreased soil pH, SOC and TN, and significantly increased soil EC, P and K, and soil properties varied significantly with different cultivation years. Grassland reclamation increases the diversity of bacterial communities, the relative abundance of Proteobacteria, Gemmatimonadetes and Bacteroidetes increased, while that of Actinobacteria, Acidobacteria, Rokubacteria and Verrucomicrobia decreased. However, the relative abundance of Proteobacteria decreased and the relative abundance of Chloroflexi and Nitrospirae increased with the increase of cultivated land years. Mantel test and RDA analysis showed that TP, AP, SOC and EC were the main factors affecting the diversity of composition of bacterial communities. In conclusion, soil properties and bacterial communities were significantly altered after long-term cultivation. This study provides data support for land use and grassland ecological protection in this region.
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15
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Venturini AM, Dias NMS, Gontijo JB, Yoshiura CA, Paula FS, Meyer KM, Nakamura FM, da França AG, Borges CD, Barlow J, Berenguer E, Nüsslein K, Rodrigues JLM, Bohannan BJM, Tsai SM. Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon. ENVIRONMENTAL RESEARCH 2022; 212:113139. [PMID: 35337832 DOI: 10.1016/j.envres.2022.113139] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 02/24/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.
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Affiliation(s)
- Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil; Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, 08544, USA.
| | - Naissa M S Dias
- Environmental Biogeochemistry Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil; Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, SP, 05508-120, Brazil
| | - Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA; Department of Integrative Biology, University of California - Berkeley, Berkeley, CA, 94720, USA
| | - Fernanda M Nakamura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Aline G da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Clovis D Borges
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Erika Berenguer
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK; Environmental Change Institute, University of Oxford, Oxford, OX1 3QY, UK
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Jorge L M Rodrigues
- Department of Land, Air, and Water Resources, University of California - Davis, Davis, CA, 95616, USA
| | - Brendan J M Bohannan
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
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16
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Huber KJ, Pester M, Eichorst SA, Navarrete AA, Foesel BU. Editorial: Acidobacteria – Towards Unraveling the Secrets of a Widespread, Though Enigmatic, Phylum. Front Microbiol 2022; 13:960602. [PMID: 35814658 PMCID: PMC9267355 DOI: 10.3389/fmicb.2022.960602] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Katharina J. Huber
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael Pester
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Stephanie A. Eichorst
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Acacio A. Navarrete
- Graduate Program in Environmental Sciences, University Brazil, São Paulo, Brazil
| | - Bärbel U. Foesel
- Working Group Biobank, Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- *Correspondence: Bärbel U. Foesel
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17
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Kimeklis A, Gladkov G, Tembotov R, Kichko A, Pinaev A, Hosid S, Andronov E, Abakumov E. Microbiome composition of disturbed soils from sandy-gravel mining complexes with different reclamation approaches. ONE ECOSYSTEM 2022. [DOI: 10.3897/oneeco.7.e83756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Activities connected to mineral mining disrupt the soil layer and bring parent rock material to the surface. It leads to altering the environmental conditions and leaves behind vast areas of disturbed lands. Returning these lands to natural ecosystems is an important contemporary challenge, which can be acquired by reclamation practices. Soil microbiome composition reflects changes happening to disturbed lands; thus, its analysis is a powerful tool for evaluating the disturbance degree and estimating the effect of the implementation of reclamation techniques. Additionally, factors connected to the characteristics of a particular geographical region have a certain impact on the microbiome and should be taken into account. Thereby, studies of soil microbiomes of disturbed soils of different origins are essential in understanding the dynamics of soil restoration. Here, we focus on soil microbiomes from two sandy-gravel mining complexes in mountainous areas with a moderate continental climate of the Central Caucasus. These quarries share the same parent rock material, but differ in benchmark soil type and reclamation approach - one was left for passive recovery and the other was technically reclaimed with overburden material. Comparative analysis of microbiome composition, based on sequencing of 16S rRNA gene libraries, showed that region and disturbance are the key factors explaining microbiome variation, which surpass the influence of local factors. However, the application of reclamation techniques greatly reduces the dissimilarity of soil microbiomes caused by disturbance. Linking of soil chemical parameters to microbiome composition showed that the disturbance factor correlates with a lack of organic carbon. Other chemical parameters, like pH, ammonium, nitrates and total carbon explain microbiome variability on a smaller scale between sampling sites. Thus, while regional and disturbance factors reflected differentiation of soil microbiomes, soil chemical parameters explained local variation of certain groups of microorganisms.
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18
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Hariharan J, Buckley DH. Elevational Gradients Impose Dispersal Limitation on Streptomyces. Front Microbiol 2022; 13:856263. [PMID: 35592003 PMCID: PMC9113539 DOI: 10.3389/fmicb.2022.856263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
Dispersal governs microbial biogeography, but the rates and mechanisms of dispersal remain poorly characterized for most microbial taxa. Dispersal limitation is driven by limits on dissemination and establishment, respectively. Elevation gradients create striking patterns of biogeography because they produce steep environmental gradients at small spatial scales, and these gradients offer a powerful tool to examine mechanisms of dispersal limitation. We focus on Streptomyces, a bacterial genus common to soil, by using a taxon-specific phylogenetic marker, the RNA polymerase-encoding rpoB gene. By targeting Streptomyces, we assess dispersal limitation at finer phylogenetic resolution than is possible using whole community analyses. We characterized Streptomyces diversity at local spatial scales (100 to 3,000 m) in two temperate forest sites located in the Adirondacks region of New York State: Woods Lake (<100 m elevation change), and Whiteface Mountain (>1,000 m elevation change). Beta diversity varied considerably at both locations, indicative of dispersal limitation acting at local spatial scales, but beta diversity was significantly higher at Whiteface Mountain. Beta diversity varied across elevation at Whiteface Mountain, being lowest at the mountain’s base. We show that Streptomyces taxa exhibit elevational preferences, and these preferences are phylogenetically conserved. These results indicate that habitat preferences influence Streptomyces biogeography and suggest that barriers to establishment structure Streptomyces communities at higher elevations. These data illustrate that Streptomyces biogeography is governed by dispersal limitation resulting from a complex mixture of stochastic and deterministic processes.
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Affiliation(s)
- Janani Hariharan
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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19
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Zhou Z, Wu H, Li D, Zeng W, Huang J, Wu Z. Comparison of gut microbiome in the Chinese mud snail ( Cipangopaludina chinensis) and the invasive golden apple snail ( Pomacea canaliculata). PeerJ 2022; 10:e13245. [PMID: 35402093 PMCID: PMC8992660 DOI: 10.7717/peerj.13245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/18/2022] [Indexed: 01/13/2023] Open
Abstract
Background Gut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level. Methods Gut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3-V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing. Results The gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail.
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Affiliation(s)
- Zihao Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Hongying Wu
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Dinghong Li
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Wenlong Zeng
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Jinlong Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China,College of Life Sciences, Guangxi Normal University, Guilin, Guangxi, China
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
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20
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Jones CM, Putz M, Tiemann M, Hallin S. Reactive nitrogen restructures and weakens microbial controls of soil N2O emissions. Commun Biol 2022; 5:273. [PMID: 35347224 PMCID: PMC8960841 DOI: 10.1038/s42003-022-03211-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/02/2022] [Indexed: 12/20/2022] Open
Abstract
AbstractThe global surplus of reactive nitrogen (Nr) in agricultural soils is accelerating nitrous oxide (N2O) emission rates, and may also strongly influence the microbial controls of this greenhouse gas resulting in positive feedbacks that further exacerbate N2O emissions. Yet, the link between legacy effects of Nr on microbial communities and altered regulation of N2O emissions is unclear. By examining soils with legacies of Nr-addition from 14 field experiments with different edaphic backgrounds, we show that increased potential N2O production is associated with specific phylogenetic shifts in communities of frequently occurring soil microbes. Inputs of Nr increased the complexity of microbial co-association networks, and altered the relative importance of biotic and abiotic predictors of potential N2O emissions. Our results provide a link between the microbial legacy of Nr addition and increased N2O emissions by demonstrating that biological controls of N2O emissions were more important in unfertilized soils and that these controls are weakened by increasing resource levels in soil.
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21
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Sauer HM, Hamilton TL, Anderson RE, Umbanhowar CE, Heathcote AJ. Diversity and distribution of sediment bacteria across an ecological and trophic gradient. PLoS One 2022; 17:e0258079. [PMID: 35312685 PMCID: PMC8936460 DOI: 10.1371/journal.pone.0258079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/04/2022] [Indexed: 11/18/2022] Open
Abstract
The microbial communities of lake sediments have the potential to serve as valuable bioindicators and integrators of watershed land-use and water quality; however, the relative sensitivity of these communities to physio-chemical and geographical parameters must be demonstrated at taxonomic resolutions that are feasible by current sequencing and bioinformatic approaches. The geologically diverse and lake-rich state of Minnesota (USA) is uniquely situated to address this potential because of its variability in ecological region, lake type, and watershed land-use. In this study, we selected twenty lakes with varying physio-chemical properties across four ecological regions of Minnesota. Our objectives were to (i) evaluate the diversity and composition of the bacterial community at the sediment-water interface and (ii) determine how lake location and watershed land-use impact aqueous chemistry and influence bacterial community structure. Our 16S rRNA amplicon data from lake sediment cores, at two depth intervals, data indicate that sediment communities are more likely to cluster by ecological region rather than any individual lake properties (e.g., trophic status, total phosphorous concentration, lake depth). However, composition is tied to a given lake, wherein samples from the same core were more alike than samples collected at similar depths across lakes. Our results illustrate the diversity within lake sediment microbial communities and provide insight into relationships between taxonomy, physicochemical, and geographic properties of north temperate lakes.
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Affiliation(s)
- Hailey M. Sauer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- St. Croix Watershed Research Station, Science Museum of Minnesota, Marine on St. Croix, Minnesota, United States of America
| | - Trinity L. Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- The Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
| | - Rika E. Anderson
- Biology Department, Carleton College, Northfield, Minnesota, United States of America
| | - Charles E. Umbanhowar
- Department of Biology and Environmental Studies, St. Olaf College, Northfield, Minnesota, United States of America
| | - Adam J. Heathcote
- St. Croix Watershed Research Station, Science Museum of Minnesota, Marine on St. Croix, Minnesota, United States of America
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Wang G, Li Y, Liu J, Chen B, Su H, Liang J, Huang W, Yu K. Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov. Front Microbiol 2022; 13:778535. [PMID: 35173698 PMCID: PMC8841776 DOI: 10.3389/fmicb.2022.778535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Members of the phylum Acidobacteria are ubiquitous in various environments. Soil acidobacteria have been reported to present a variety of strategies for their success in terrestrial environments. However, owing to lack of pure culture, information on animal-associated acidobacteria are limited, except for those obtained from 16S rRNA genes. To date, only two acidobacteria have been isolated from animals, namely strain M133T obtained from coral Porites lutea and Acanthopleuribacter pedis KCTC 12899T isolated from chiton. Genomics and physiological characteristics of strain M133T and A. pedis KCTC 12899T were compared with 19 other isolates (one strain from each genus) in the phylum Acidobacteria. The results revealed that strain M133T represents a new species in a new genus in the family Acanthopleuribacteraceae. To date, these two Acanthopleuribacteraceae isolates have the largest genomes (10.85–11.79 Mb) in the phylum Acidobacteria. Horizontal gene transfer and gene duplication influenced the structure and plasticity of these large genomes. Dissimilatory nitrate reduction and abundant secondary metabolite biosynthetic gene clusters (including eicosapentaenoic acid de novo biosynthesis) are two distinct features of the Acanthopleuribacteraceae bacteria in the phylum Acidobacteria. The absence of glycoside hydrolases involved in plant polysaccharide degradation and presence of animal disease-related peptidases indicate that these bacteria have evolved to adapt to the animal hosts. In addition to low- and high-affinity respiratory oxygen reductases, enzymes for nitrate to nitrogen, and sulfhydrogenase were also detected in strain M133T, suggesting the capacity and flexibility to grow in aerobic and anaerobic environments. This study highlighted the differences in genome structure, carbohydrate and protein utilization, respiration, and secondary metabolism between animal-associated acidobacteria and other acidobacteria, especially the soil acidobacteria, displaying flexibility and versatility of the animal-associated acidobacteria in environmental adaption.
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Affiliation(s)
- Guanghua Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Yuanjin Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Jianfeng Liu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Biao Chen
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Hongfei Su
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Wen Huang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
- Coral Reef Research Center of China, Guangxi University, Nanning, China
- School of Marine Sciences, Guangxi University, Nanning, China
- *Correspondence: Kefu Yu,
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23
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Li R, Liu Y, Cheng J, Xue N, Sun Z, Zhang P, Li N, Di X, Fan W, Deng J, Ma Y, Li M, Sheng J. Distinct soil bacterial patterns along narrow and broad elevational gradients in the grassland of Mt. Tianshan, China. Sci Rep 2022; 12:136. [PMID: 34997011 PMCID: PMC8742048 DOI: 10.1038/s41598-021-03937-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 12/13/2021] [Indexed: 12/01/2022] Open
Abstract
Bacteria are essential regulators of soil biogeochemical cycles. While several studies of bacterial elevational patterns have been performed in recent years, the drivers of these patterns remain incompletely understood. To clarify bacterial distribution patterns and diversity across narrow- and broad-scale elevational gradients, we collected soil samples from 22 sites in the grasslands of Mt. Tianshan in China along three elevational transects and the overall elevation transect: (1) 6 sites at elevations of 1047–1587 m, (2) 8 sites at 876–3070 m, and (3) 8 sites at 1602–2110 m. The bacterial community diversity across the overall elevation transects exhibited a hump-like pattern, whereas consistent patterns were not observed in the separate elevational transects. The bacterial community composition at the phylum level differed across the transects and elevation sites. The Actinobacteria was the most abundant phylum overall (41.76%) but showed clear variations in the different transects. Furthermore, heatmap analyses revealed that both pH and mean annual temperature (MAT) were significantly (P < 0.05) correlated with bacterial community composition as well as the dominant bacterial phyla, classes, and genera. These findings provide an inclusive view of bacterial community structures in relation to the environmental factors of the different elevational patterns.
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Affiliation(s)
- Rui Li
- College of Grassland and Environmental Sciences, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, Xinjiang, China.,Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China
| | - Yunhua Liu
- College of Grassland and Environmental Sciences, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, Xinjiang, China.,Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China
| | - Junhui Cheng
- College of Grassland and Environmental Sciences, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, Xinjiang, China.,Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China
| | - Nana Xue
- College of Grassland and Environmental Sciences, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, Xinjiang, China.,Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China
| | - Zongjiu Sun
- Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China
| | - Pan Zhang
- College of Grassland and Environmental Sciences, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, Xinjiang, China.,Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China
| | - Ning Li
- Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China
| | - Xiaoshuang Di
- Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China
| | - Weihua Fan
- Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China
| | - Jiang Deng
- Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China
| | - Yucheng Ma
- Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China
| | - Minfei Li
- Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China
| | - Jiandong Sheng
- College of Grassland and Environmental Sciences, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, Xinjiang, China. .,Key Laboratory of Soil and Plant Ecological Processes of Xinjiang, Urumqi, 830052, Xinjiang, China.
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24
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Chiba A, Uchida Y, Kublik S, Vestergaard G, Buegger F, Schloter M, Schulz S. Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition. Microorganisms 2021; 9:microorganisms9020357. [PMID: 33670245 PMCID: PMC7916959 DOI: 10.3390/microorganisms9020357] [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: 01/26/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.
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Affiliation(s)
- Akane Chiba
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Crop Physiology, TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Yoshitaka Uchida
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Correspondence: ; Tel.: +49-(0)89-3187-3054
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25
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Chen T, Hu R, Zheng Z, Yang J, Fan H, Deng X, Yao W, Wang Q, Peng S, Li J. Soil Bacterial Community in the Multiple Cropping System Increased Grain Yield Within 40 Cultivation Years. FRONTIERS IN PLANT SCIENCE 2021; 12:804527. [PMID: 34987540 PMCID: PMC8721226 DOI: 10.3389/fpls.2021.804527] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/22/2021] [Indexed: 05/05/2023]
Abstract
The shortage of land resources restricts the sustainable development of agricultural production. Multiple cropping has been widely used in Southern China, but whether the continuous planting will cause a decline in soil quality and crop yield is unclear. To test whether multiple cropping could increase grain yield, we investigated the farmlands with different cultivation years (10-20 years, 20-40 years, and >40 years). Results showed that tobacco-rice multiple cropping rotation significantly increased soil pH, nitrogen nutrient content, and grain yield, and it increased the richness of the bacterial community. The farmland with 20-40 years of cultivation has the highest soil organic carbon (SOC), ammonium nitrogen, and grain yield, but there is no significant difference in the diversity and structure of the bacterial community in farmlands with different cultivation years. The molecular ecological network indicated that the stability of the bacterial community decreased across the cultivation years, which may result in a decline of farmland yields in multiple cropping system> 40 years. The Acidobacteria members as the keystone taxa (Zi ≥ 2.5 or Pi ≥ 0.62) appeared in the tobacco-rice multiple cropping rotation farmlands, and the highest abundance of Acidobacteria was found in the farmland with the highest SOC and ammonium nitrogen content, suggesting Acidobacteria Gp4, GP7, GP12, and GP17 are important taxa involved in the soil carbon and nitrogen cycle. Therefore, in this study, the multiple cropping systems for 20 years will not reduce the crop production potential, but they cannot last for more than 40 years. This study provides insights for ensuring soil quality and enhancing sustainable agricultural production capacity.
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Affiliation(s)
- Tao Chen
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Hunan Tobacco Company Chenzhou Branch, Chenzhou, China
| | - Ruiwen Hu
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Zhongyi Zheng
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jiayi Yang
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Huan Fan
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | | | - Wang Yao
- Hunan Tobacco Company Zhangjiajie Branch, Zhangjiajie, China
| | - Qiming Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Shuguang Peng
- Hunan Tobacco Monopoly Bureau, Changsha, China
- *Correspondence: Shuguang Peng
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Juan Li
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26
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Taskin E, Boselli R, Fiorini A, Misci C, Ardenti F, Bandini F, Guzzetti L, Panzeri D, Tommasi N, Galimberti A, Labra M, Tabaglio V, Puglisi E. Combined Impact of No-Till and Cover Crops with or without Short-Term Water Stress as Revealed by Physicochemical and Microbiological Indicators. BIOLOGY 2021; 10:biology10010023. [PMID: 33401423 PMCID: PMC7824270 DOI: 10.3390/biology10010023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 01/05/2023]
Abstract
Simple Summary Farming systems in which no-till (NT) and cover crops (CC) are preferred as alternatives to conventional practices have the promise of being more resilient and climate smart. Our field study aimed to assess the long-term impact of NT plus CC, with vs. without short-term water stress, on soil microbial biodiversity, enzymatic activities, and the distribution of C and N pools within soil aggregates. We found that the diversity of bacteria and fungi in the soil was positively affected by NT + CC, especially under water stress conditions. Under NT + CC, the presence of important plant growth-promoting rhizobacteria was revealed. Soil enzymatic activity confirmed the depleting impact of conventional tillage. Soil C and N were increased under NT + CC due to their inclusion into large soil aggregates that are beneficial for long-term C and N stabilization in soils. Water stress was found to have detrimental effects on aggregates formation and limited C and N inclusion within aggregates. The microbiological and physicochemical parameters correlation supported the hypothesis that long-term NT + CC is a valuable strategy for sustainable agroecosystems, due to its contribution to soil C and N stabilization while enhancing the biodiversity and enzymes. Abstract Combining no-till and cover crops (NT + CC) as an alternative to conventional tillage (CT) is generating interest to build-up farming systems’ resilience while promoting climate change adaptation in agriculture. Our field study aimed to assess the impact of long-term NT + CC management and short-term water stress on soil microbial communities, enzymatic activities, and the distribution of C and N within soil aggregates. High-throughput sequencing (HTS) revealed the positive impact of NT + CC on microbial biodiversity, especially under water stress conditions, with the presence of important rhizobacteria (e.g., Bradyrhizobium spp.). An alteration index based on soil enzymes confirmed soil depletion under CT. C and N pools within aggregates showed an enrichment under NT + CC mostly due to C and N-rich large macroaggregates (LM), accounting for 44% and 33% of the total soil C and N. Within LM, C and N pools were associated to microaggregates within macroaggregates (mM), which are beneficial for long-term C and N stabilization in soils. Water stress had detrimental effects on aggregate formation and limited C and N inclusion within aggregates. The microbiological and physicochemical parameters correlation supported the hypothesis that long-term NT + CC is a promising alternative to CT, due to the contribution to soil C and N stabilization while enhancing the biodiversity and enzymes.
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Affiliation(s)
- Eren Taskin
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Roberta Boselli
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (R.B.); (A.F.); (F.A.)
| | - Andrea Fiorini
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (R.B.); (A.F.); (F.A.)
| | - Chiara Misci
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Federico Ardenti
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (R.B.); (A.F.); (F.A.)
| | - Francesca Bandini
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Lorenzo Guzzetti
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Davide Panzeri
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Nicola Tommasi
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Andrea Galimberti
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Massimo Labra
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Vincenzo Tabaglio
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (R.B.); (A.F.); (F.A.)
- Correspondence: ; Tel.: +39-05-2359-9222
| | - Edoardo Puglisi
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
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27
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Di Marcantonio C, Bertelkamp C, van Bel N, Pronk TE, Timmers PHA, van der Wielen P, Brunner AM. Organic micropollutant removal in full-scale rapid sand filters used for drinking water treatment in The Netherlands and Belgium. CHEMOSPHERE 2020; 260:127630. [PMID: 32758778 DOI: 10.1016/j.chemosphere.2020.127630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/19/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
Biological treatment processes have the potential to remove organic micropollutants (OMPs) during water treatment. The OMP removal capacity of conventional drinking water treatment processes such as rapid sand filters (RSFs), however, has not been studied in detail. We investigated OMP removal and transformation product (TP) formation in seven full-scale RSFs all treating surface water, using high-resolution mass spectrometry based quantitative suspect and non-target screening (NTS). Additionally, we studied the microbial communities with 16S rRNA gene amplicon sequencing (NGS) in both influent and effluent waters as well as the filter medium, and integrated these data to comprehensively assess the processes that affect OMP removal. In the RSF influent, 9 to 30 of the 127 target OMPs were detected. The removal efficiencies ranged from 0 to 93%. A data-driven workflow was established to monitor TPs, based on the combination of NTS feature intensity profiles between influent and effluent samples and the prediction of biotic TPs. The workflow identified 10 TPs, including molecular structure. Microbial community composition analysis showed similar community composition in the influent and effluent of most RSFs, but different from the filter medium, implying that specific microorganisms proliferate in the RSFs. Some of these are able to perform typical processes in water treatment such as nitrification and iron oxidation. However, there was no clear relationship between OMP removal efficiency and microbial community composition. The innovative combination of quantitative analyses, NTS and NGS allowed to characterize real scale biological water treatments, emphasizing the potential of bio-stimulation applications in drinking water treatment.
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Affiliation(s)
- Camilla Di Marcantonio
- Sapienza University of Rome, Department of Civil, Constructional and Environmental Engineering (DICEA), Rome, Italy
| | - Cheryl Bertelkamp
- KWR Water Research Institute, P.O. Box 1072, 3430, BB, Nieuwegein, the Netherlands
| | - Nikki van Bel
- KWR Water Research Institute, P.O. Box 1072, 3430, BB, Nieuwegein, the Netherlands
| | - Tessa E Pronk
- KWR Water Research Institute, P.O. Box 1072, 3430, BB, Nieuwegein, the Netherlands
| | - Peer H A Timmers
- KWR Water Research Institute, P.O. Box 1072, 3430, BB, Nieuwegein, the Netherlands
| | - Paul van der Wielen
- KWR Water Research Institute, P.O. Box 1072, 3430, BB, Nieuwegein, the Netherlands; Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, the Netherlands
| | - Andrea M Brunner
- KWR Water Research Institute, P.O. Box 1072, 3430, BB, Nieuwegein, the Netherlands.
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Hermans SM, Taylor M, Grelet G, Curran-Cournane F, Buckley HL, Handley KM, Lear G. From pine to pasture: land use history has long-term impacts on soil bacterial community composition and functional potential. FEMS Microbiol Ecol 2020; 96:5807072. [PMID: 32175557 DOI: 10.1093/femsec/fiaa041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/09/2020] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities are crucial to soil ecosystems and are known to be sensitive to environmental changes. However, our understanding of how present-day soil bacterial communities remain impacted by historic land uses is limited; implications for their functional potential are especially understudied. Through 16S rRNA gene amplicon and shotgun metagenomic sequencing, we characterized the structure and functional potential of soil bacterial communities after land use conversion. Sites converted from pine plantations to dairy pasture were sampled five- and eight-years post conversion. The bacterial community composition and functional potential at these sites were compared to long-term dairy pastures and pine forest reference sites. Bacterial community composition and functional potential at the converted sites differed significantly from those at reference sites (P = 0.001). On average, they were more similar to those in the long-term dairy sites and showed gradual convergence (P = 0.001). Differences in composition and functional potential were most strongly related to nutrients such as nitrogen, Olsen P and the carbon to nitrogen ratio. Genes related to the cycling of nitrogen, especially denitrification, were underrepresented in converted sites compared to long-term pasture soils. Together, our study highlights the long-lasting impacts land use conversion can have on microbial communities, and the implications for future soil health and functioning.
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Affiliation(s)
- Syrie M Hermans
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, New Zealand
| | - Matthew Taylor
- Waikato Regional Council, 401 Grey Street, Hamilton 3216, New Zealand
| | - Gwen Grelet
- Manaaki Whenua - Landcare Research, 54 Gerald Street, Lincoln, New Zealand
| | - Fiona Curran-Cournane
- Ministry for the Environment - Manatū Mō Te Taiao, 45 Queen Street, Auckland 1010, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, 46 Wakefield St, Auckland, 1010, New Zealand
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland, New Zealand
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29
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Xie F, Zhang G, Zheng Q, Liu K, Yin X, Sun X, Saud S, Shi Z, Yuan R, Deng W, Zhang L, Cui G, Chen Y. Beneficial Effects of Mixing Kentucky Bluegrass With Red Fescue via Plant-Soil Interactions in Black Soil of Northeast China. Front Microbiol 2020; 11:556118. [PMID: 33193137 PMCID: PMC7656059 DOI: 10.3389/fmicb.2020.556118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/28/2020] [Indexed: 12/26/2022] Open
Abstract
Continuous monoculture of cool-season turfgrass causes soil degradation, and visual turf quality decline is a major concern in black soil regions of Northeast China. Turf mixtures can enhance turfgrass resistance to biotic and abiotic stresses and increase soil microbial diversity. Understanding mechanism by plant-soil interactions and changes of black soil microbial communities in turf mixture is beneficial to restoring the degradation of urbanized black soils and maintaining sustainable development of urban landscape ecology. In this study, based on the previous research of different sowing models, two schemes of turf monoculture and mixture were conducted in field plots during 2016-2018 in a black soil of Heilongjiang province of Northeast China. The mixture turf was established by mixing 50% Kentucky bluegrass "Midnight" (Poa pratensis L.) with 50% Red fescue "Frigg" (Festuca rubra L.); and the monoculture turf was established by sowing with pure Kentucky bluegrass. Turf performance, soil physiochemical properties, and microbial composition from rhizosphere were investigated. Soil microbial communities and abundance were analyzed by Illumina MiSeq sequencing and quantitative PCR methods. Results showed that turfgrass quality, turfgrass biomass, soil organic matter (SOM), urease, alkaline phosphatase, invertase, and catalase activities increased in PF mixture, but disease percentage and soil pH decreased. The microbial diversity was also significantly enhanced under turf mixture model. The microbial community compositions were significantly different between the two schemes. Turf mixtures obviously increased the abundances of Beauveria, Lysobacter, Chryseolinea, and Gemmatimonas spp., while remarkably reduced the abundances of Myrothecium and Epicoccum spp. Redundancy analysis showed that the compositions of bacteria and fungi were related to edaphic parameters, such as SOM, pH, and enzyme activities. Since the increasing of turf quality, biomass, and disease resistance were highly correlated with the changes of soil physiochemical parameters and microbial communities in turf mixture, which suggested that turf mixture with two species (i.e., Kentucky blue grass and Red fescue) changed soil microbial communities and enhanced visual turfgrass qualities through positive plant-soil interactions by soil biota.
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Affiliation(s)
- Fuchun Xie
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Gaoyun Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Qianjiao Zheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Kemeng Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China.,Beijing Oriental Garden Environment Co., Ltd, Beijing, China
| | - Xiujie Yin
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xiaoyang Sun
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Shah Saud
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Zhenjie Shi
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Runli Yuan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Wenjing Deng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Lu Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yajun Chen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
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Biological invasions alter environmental microbiomes: A meta-analysis. PLoS One 2020; 15:e0240996. [PMID: 33091062 PMCID: PMC7580985 DOI: 10.1371/journal.pone.0240996] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
Biological invasions impact both agricultural and natural systems. The damage can be quantified in terms of both economic loss and reduction of biodiversity. Although the literature is quite rich about the impact of invasive species on plant and animal communities, their impact on environmental microbiomes is underexplored. Here, we re-analyze publicly available data using a common framework to create a global synthesis of the effects of biological invasions on environmental microbial communities. Our findings suggest that non-native species are responsible for the loss of microbial diversity and shifts in the structure of microbial populations. Therefore, the impact of biological invasions on native ecosystems might be more pervasive than previously thought, influencing both macro- and micro-biomes. We also identified gaps in the literature which encourage research on a wider variety of environments and invaders, and the influence of invaders across seasons and geographical ranges.
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31
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Lee SA, Kim JM, Kim Y, Joa JH, Kang SS, Ahn JH, Kim M, Song J, Weon HY. Different types of agricultural land use drive distinct soil bacterial communities. Sci Rep 2020; 10:17418. [PMID: 33060673 PMCID: PMC7562711 DOI: 10.1038/s41598-020-74193-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/20/2020] [Indexed: 01/11/2023] Open
Abstract
Biogeographic patterns in soil bacterial communities and their responses to environmental variables are well established, yet little is known about how different types of agricultural land use affect bacterial communities at large spatial scales. We report the variation in bacterial community structures in greenhouse, orchard, paddy, and upland soils collected from 853 sites across the Republic of Korea using 16S rRNA gene pyrosequencing analysis. Bacterial diversities and community structures were significantly differentiated by agricultural land-use types. Paddy soils, which are intentionally flooded for several months during rice cultivation, had the highest bacterial richness and diversity, with low community variation. Soil chemical properties were dependent on agricultural management practices and correlated with variation in bacterial communities in different types of agricultural land use, while the effects of spatial components were little. Firmicutes, Chloroflexi, and Acidobacteria were enriched in greenhouse, paddy, and orchard soils, respectively. Members of these bacterial phyla are indicator taxa that are relatively abundant in specific agricultural land-use types. A relatively large number of taxa were associated with the microbial network of paddy soils with multiple modules, while the microbial network of orchard and upland soils had fewer taxa with close mutual interactions. These results suggest that anthropogenic agricultural management can create soil disturbances that determine bacterial community structures, specific bacterial taxa, and their relationships with soil chemical parameters. These quantitative changes can be used as potential biological indicators for monitoring the impact of agricultural management on the soil environment.
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Affiliation(s)
- Shin Ae Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Jeong Myeong Kim
- Water Supply and Sewerage Research Division, National Institute of Environmental Research, Incheon, Republic of Korea
| | - Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Jae-Ho Joa
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeju, Republic of Korea
| | - Seong-Soo Kang
- Soil and Fertilization Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Jae-Hyung Ahn
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Mincheol Kim
- Korea Polar Research Institute, Incheon, Republic of Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea.
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32
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Seasonal and Agricultural Response of Acidobacteria Present in Two Fynbos Rhizosphere Soils. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12070277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Acidobacteria is one of the most abundant phyla in most soil types. Fynbos plants are endemic to South Africa, and these soils provide the ideal habitat for Acidobacteria, because of its low pH and oligotrophic properties. However, little is known about their distribution in the fynbos biome and the impact of cultivation of plants on Acidobacterial diversity. Therefore, the aim of this study was to determine the effect of seasonal changes and cultivation on the relative abundance and diversity of Acidobacteria associated with Aspalathus linearis (rooibos) and Cyclopia spp. (honeybush). This study was based on rhizosphere soil. A total of 32 and 31 operational taxonomic units (OTUs) were identified for honeybush and rooibos, respectively. The majority of these were classified as representatives of subdivisions 1, 2, 3, and 10. Significant differences in community compositions were observed between seasons for both honeybush and rooibos, as well as between the cultivated and uncultivated honeybush. Acidobacteria had a significantly positive correlation with pH, C, Ca2+, and P. In this study, we have shown the effect of seasonal changes, in summer and winter, and cultivation farming on the relative abundance and diversity of Acidobacteria present in the soil of rooibos and honeybush.
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33
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Effects of elk and bison carcasses on soil microbial communities and ecosystem functions in Yellowstone, USA. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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34
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Diazotrophs Show Signs of Restoration in Amazon Rain Forest Soils with Ecosystem Rehabilitation. Appl Environ Microbiol 2020; 86:AEM.00195-20. [PMID: 32169937 DOI: 10.1128/aem.00195-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/08/2020] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation can be an important source of nitrogen in tropical forests that serve as a major CO2 sink. Extensive deforestation of the Amazon is known to influence microbial communities and the biogeochemical cycles they mediate. However, it is unknown how diazotrophs (nitrogen-fixing microorganisms) respond to deforestation and subsequent ecosystem conversion to agriculture, as well as whether they can recover in secondary forests that are established after agriculture is abandoned. To address these knowledge gaps, we combined a spatially explicit sampling approach with high-throughput sequencing of nifH genes. The main objectives were to assess the functional distance decay relationship of the diazotrophic bacterial community in a tropical forest ecosystem and to quantify the roles of various factors that drive the observed changes in the diazotrophic community structure. We observed an increase in local diazotrophic diversity (α-diversity) with a decrease in community turnover (β-diversity), associated with a shift in diazotrophic community structure as a result of the forest-to-pasture conversion. Both diazotrophic community turnover and structure showed signs of recovery in secondary forests. Changes in the diazotrophic community were primarily driven by the change in land use rather than differences in geochemical characteristics or geographic distances. The diazotroph communities in secondary forests resembled those in primary forests, suggesting that at least partial recovery of diazotrophs is possible following agricultural abandonment.IMPORTANCE The Amazon region is a major tropical forest region that is being deforested at an alarming rate to create space for cattle ranching and agriculture. Diazotrophs (nitrogen-fixing microorganisms) play an important role in supplying soil N for plant growth in tropical forests. It is unknown how diazotrophs respond to deforestation and whether they can recover in secondary forests that establish after agriculture is abandoned. Using high-throughput sequencing of nifH genes, we characterized the response of diazotrophs' β-diversity and identified major drivers of changes in diazotrophs from forest-to-pasture and pasture-to-secondary-forest conversions. Studying the impact of land use change on diazotrophs is important for a better understanding of the impact of deforestation on tropical forest ecosystem functioning, and our results on the potential recovery of diazotrophs in secondary forests imply the possible restoration of ecosystem functions in secondary forests.
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35
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Venturini AM, Nakamura FM, Gontijo JB, da França AG, Yoshiura CA, Mandro JA, Tsai SM. Robust DNA protocols for tropical soils. Heliyon 2020; 6:e03830. [PMID: 32426533 PMCID: PMC7226647 DOI: 10.1016/j.heliyon.2020.e03830] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 09/06/2019] [Accepted: 04/21/2020] [Indexed: 12/14/2022] Open
Abstract
Studies in the Amazon are being intensified to evaluate the alterations in the microbial communities of soils and sediments in the face of increasing deforestation and land-use changes in the region. However, since these environments present highly heterogeneous physicochemical properties, including contaminants that hinder nucleic acids isolation and downstream techniques, the development of best molecular practices is crucial. This work aimed to optimize standard protocols for DNA extraction and gene quantification by quantitative real-time PCR (qPCR) based on natural and anthropogenic soils and sediments (primary forest, pasture, Amazonian Dark Earth, and várzea, a seasonally flooded area) of the Eastern Amazon. Our modified extraction protocol increased the fluorometric DNA concentration by 48%, reaching twice the original amount for most of the pasture and várzea samples, and the 260/280 purity ratio by 15% to values between 1.8 to 2.0, considered ideal for DNA. The addition of bovine serum albumin in the qPCR reaction improved the quantification of the 16S rRNA genes of Archaea and Bacteria and its precision among technical replicates, as well as allowed their detection in previously non-amplifiable samples. It is concluded that the changes made in the protocols improved the parameters of the DNA samples and their amplification, thus increasing the reliability of microbial communities' analysis and its ecological interpretations.
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Affiliation(s)
- Andressa Monteiro Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Fernanda Mancini Nakamura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Júlia Brandão Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Aline Giovana da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Caio Augusto Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Jéssica Adriele Mandro
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário, 303, Piracicaba, SP, 13416-000, Brazil
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36
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Fang Y, Vanzin G, Cupples AM, Strathmann TJ. Influence of terminal electron-accepting conditions on the soil microbial community and degradation of organic contaminants of emerging concern. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135327. [PMID: 31846887 DOI: 10.1016/j.scitotenv.2019.135327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
Better understanding of the fate and persistence of trace organic contaminants of emerging concern (CEC) in agricultural soils is critical for assessing the risks associated with using treated wastewater effluent to irrigate crops and land application of wastewater biosolids. This study reports on the influence of prevailing terminal electron-accepting processes (TEAPs, i.e., aerobic, nitrate-reducing, iron(III)-reducing, and sulfate-reducing conditions) and exposure to a mixture of nine trace CEC (90 ng/g each) on both the microbial community structure and CEC degradation in agricultural soil. DNA analysis revealed significant differences in microbial community composition following establishment of different TEAPs, but no significant change upon exposure to the mixture of CEC. The largest community shift was observed after establishing nitrate-reducing conditions and the smallest shift for sulfate-reducing conditions. Two of the CEC (atrazine and sulfamethoxazole) showed significant degradation in both bioactive and abiotic (i.e., sterilized) conditions, with half-lives ranging from 1 to 64 days for different TEAPs, while six of the CEC (amitriptyline, atenolol, trimethoprim, and three organophosphate flame retardants) only degraded in bioactive samples, with half-lives ranging from 27 to 90 days; carbamazepine did not degrade appreciably within 90 days in any of the incubations. Amplicon sequence variants (ASVs) from Firmicutes Hydrogenispora, Gemmatimonadetes Gemmatimonadaceae, and Verrucomicrobia OPB34 soil group were identified as potentially responsible for the biodegradation of organophosphate flame retardants, and ASVs from other taxa groups were suspected to be involved in biodegrading the other target CEC. These results demonstrate that CEC fate and persistence in agricultural soils is influenced by the prevailing TEAPs and their influence on the microbial community, suggesting the need to incorporate these factors into contaminant fate models to improve risk assessment predictions.
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Affiliation(s)
- Yida Fang
- Colorado School of Mines, Department of Civil & Environmental Engineering, 1012 14th Street, Golden, CO 80401, United States.
| | - Gary Vanzin
- Colorado School of Mines, Department of Civil & Environmental Engineering, 1012 14th Street, Golden, CO 80401, United States.
| | - Alison M Cupples
- Michigan State University, Department of Civil and Environmental Engineering, 1449 Engineering Research Court, East Lansing, MI 48824, United States.
| | - Timothy J Strathmann
- Colorado School of Mines, Department of Civil & Environmental Engineering, 1012 14th Street, Golden, CO 80401, United States.
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37
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Burges A, Fievet V, Oustriere N, Epelde L, Garbisu C, Becerril JM, Mench M. Long-term phytomanagement with compost and a sunflower - Tobacco rotation influences the structural microbial diversity of a Cu-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 700:134529. [PMID: 31693956 DOI: 10.1016/j.scitotenv.2019.134529] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
At a former wood preservation site contaminated with Cu, various phytomanagement options have been assessed in the last decade through physicochemical, ecotoxicological and biological assays. In a field trial at this site, phytomanagement with a crop rotation based on tobacco and sunflower, combined with the incorporation of compost and dolomitic limestone, has proved to be efficient in Cu-associated risk mitigation, ecological soil functions recovery and net gain of economic and social benefits. To demonstrate the long-term effectiveness and sustainability of phytomanagement, we assessed here the influence of this remediation option on the diversity, composition and structure of microbial communities over time, through a metabarcoding approach. After 9 years of phytomanagement, no overall effect was identified on microbial diversity; the soil amendments, notably the repeated compost application, led to shifts in soil microbial populations. This phytomanagement option induced changes in the composition of soil microbial communities, promoting the growth of microbial groups belonging to Alphaproteobacteria, many being involved in N cycling. Populations of Nitrososphaeria, which are crucial in nitrification, as well as taxa from phyla Planctomycetacia, Chloroflexi and Gemmatimonadetes, which are tolerant to metal contamination and adapted to oligotrophic soil conditions, decreased in amended phytomanaged plots. Our study provides an insight into population dynamics within soil microbial communities under long-term phytomanagement, in line with the assessment of soil ecological functions and their recovery.
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Affiliation(s)
- Aritz Burges
- UMR BIOGECO INRA 1202, University of Bordeaux, Bât. B2, allée Geoffroy St-Hilaire, F-33615 Pessac Cedex, France; University of the Basque Country (UPV/EHU), Department of Plant Biology and Ecology, P.O. Box 644, E-48080 Bilbao, Spain.
| | - Virgil Fievet
- UMR BIOGECO INRA 1202, University of Bordeaux, Bât. B2, allée Geoffroy St-Hilaire, F-33615 Pessac Cedex, France
| | - Nadège Oustriere
- Laboratoire Génie Civil et Géoenvironnement (LGCGE), Yncréa Hauts-de-France, Institut Supérieur d'Agriculture, 48 Bld Vauban, 59046 Lille Cedex, France
| | - Lur Epelde
- NEIKER-Tecnalia, Department of Ecology and Natural Resources, Soil Microbial Ecology Group, c/ Berreaga 1, E-48160 Derio, Spain
| | - Carlos Garbisu
- NEIKER-Tecnalia, Department of Ecology and Natural Resources, Soil Microbial Ecology Group, c/ Berreaga 1, E-48160 Derio, Spain
| | - Jose María Becerril
- University of the Basque Country (UPV/EHU), Department of Plant Biology and Ecology, P.O. Box 644, E-48080 Bilbao, Spain
| | - Michel Mench
- UMR BIOGECO INRA 1202, University of Bordeaux, Bât. B2, allée Geoffroy St-Hilaire, F-33615 Pessac Cedex, France
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38
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Khan MAW, Bohannan BJM, Nüsslein K, Tiedje JM, Tringe SG, Parlade E, Barberán A, Rodrigues JLM. Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils. FEMS Microbiol Ecol 2019; 95:5211045. [PMID: 30481288 PMCID: PMC6294608 DOI: 10.1093/femsec/fiy230] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/26/2018] [Indexed: 01/28/2023] Open
Abstract
Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ≥ P ≥ 0.80, adjusted P < 0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H++Al3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.
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Affiliation(s)
- M A Wadud Khan
- Department of Biology, University of Texas, Arlington, TX 76019, USA
| | | | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | - Susannah G Tringe
- Joint Genome Institute, United States Department of Energy, Walnut Creek, CA 94598, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eloi Parlade
- Department of Land, Air and Water Resources, University of California - Davis, Davis, CA 95616, USA
| | - Albert Barberán
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721, USA
| | - Jorge L M Rodrigues
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Land, Air and Water Resources, University of California - Davis, Davis, CA 95616, USA
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39
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Chen H, Xia Q, Yang T, Bowman D, Shi W. The soil microbial community of turf: linear and nonlinear changes of taxa and N-cycling gene abundances over a century-long turf development. FEMS Microbiol Ecol 2019; 95:5184450. [PMID: 30445630 DOI: 10.1093/femsec/fiy224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/14/2018] [Indexed: 11/13/2022] Open
Abstract
Turf, consisting of closely spaced grasses and the subtending soil, is a unique ecosystem subject to intense management. Yet soil organic matter accumulates quickly and reaches equilibrium after 20 to 50 years. Resource availability is an important driver of species richness and theoretically their relationship is expected to be unimodal. In this work, we examined the effects of turf development (i.e. a 1, 15, 20 and 109 year-old chronosequence) on microbial taxon richness, community composition, and abundances of genes putatively involved in N cycling through 16S rRNA gene and ITS region amplicon sequencing. Microbial alpha-diversity remained relatively stable although soil organic C and N increased by up to 3-fold over a century-long turf development. However, both bacterial and fungal community compositions changed substantially from those in the previous land use, pine stands and along turf development. Youngest turf was closer to the oldest turf than to middle-aged ones, specifically for bacterial community. Microbial changes to resource availability were also taxonomically specific. The relative abundance of Proteobacteria was independent of resource availability; Nitrospirae increased monotonically, and Bacteroidetes, Actinobacteria and Glomeromycota varied curvilinearly. However, abundances of most taxa from the phylum to operational taxonomic unit level and N-cycling genes varied nonlinearly with turf development.
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Affiliation(s)
- Huaihai Chen
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Qing Xia
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Tianyou Yang
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Daniel Bowman
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Shi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
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40
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Li W, Liu X, Niu S. Differential responses of the acidobacterial community in the topsoil and subsoil to fire disturbance in Pinus tabulaeformis stands. PeerJ 2019; 7:e8047. [PMID: 31844567 PMCID: PMC6911345 DOI: 10.7717/peerj.8047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/16/2019] [Indexed: 11/25/2022] Open
Abstract
Acidobacteria is found to be dominant and abundant in forest soil, and performs specific ecological functions (such as cellulose decomposition and photosynthetic capacity, etc.). However, relative limited is known about its changing patterns after a fire interruption. In this study, the response of soil Acidobacteria to a wildfire disturbance was investigated using the Illumina MiSeq sequencing system. The research area was classified by different severities of fire damage (high, moderate, and low severity, and an unburnt area), and samples were collected from various soil layers (0–10 cm as topsoil; 10–20 cm as subsoil). We obtained a total of 986,036 sequence reads; 31.77% of them belonged to Acidobacteria. Overall, 18 different Acidobacteria subgroups were detected, with subgroups 4, 6, 1, 3, and 2 the most abundant, accounting for 31.55%, 30.84%, 17.42%, 6.02%, and 5.81% of acidobacterial sequences across all samples, respectively. Although no significant differences in acidobacterial diversity were found in the same soil layer across different fire severities, we observed significantly lower numbers of reads, but higher Shannon and Simpson indices, in the topsoil of the high-severity fire area than in the subsoil. Non-metric multidimensional scaling (NMDS) analysis and permutational multivariate analysis of variance (PERMANOVA) also revealed significant differences in the acidobacterial community structure between the two soil layers. Soil pH, total nitrogen, NH4+-N, the Shannon index of understory vegetation and canopy density were the major drivers for acidobacterial community structure in the topsoil, while soil pH and organic matter were significant factors in the subsoil. A variance partitioning analysis (VPA) showed that edaphic factors explained the highest variation both in the topsoil (15.6%) and subsoil (56.3%). However, there are large gaps in the understanding of this field of research that still need to be explored in future studies.
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Affiliation(s)
- Weike Li
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, China.,Fire Engineering, China Fire and Rescue Institute, Beijing, China
| | - Xiaodong Liu
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, China
| | - Shukui Niu
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, Beijing, China
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41
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Sui X, Zhang R, Frey B, Yang L, Li MH, Ni H. Land use change effects on diversity of soil bacterial, Acidobacterial and fungal communities in wetlands of the Sanjiang Plain, northeastern China. Sci Rep 2019; 9:18535. [PMID: 31811224 PMCID: PMC6898332 DOI: 10.1038/s41598-019-55063-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/18/2019] [Indexed: 12/18/2022] Open
Abstract
The bacterial, acidobacterial, and fungal communities in wetlands can undergo perturbations by various human activities, such as disturbances caused by cultivation and during the process of system restoration. In this study, we investigated the relationships between the composition of the soil bacterial, acidobacterial, and fungal communities and the transformation of wetlands by human activities in the Sanjiang Plain. Soil microbial communities were assessed in wetland soils collected from pristine marsh, neighboring cropland (wetland turned into arable land), and land that had been reforested with Larix gmelinii. The alpha-diversities of bacteria, Acidobacteria, and fungi were affected by land-use change and were highest in the arable land and lowest in the wetland soils. The soil microbial community structures were also altered with changing land-use. Canonical correlation analyses showed that beta-diversity was significantly affected by soil pH, available phosphorus, soil nitrogen, and total organic carbon. Overall, our results showed that the agricultural cultivation of wetlands changes the available soil carbon, nitrogen, and phosphorus pools, thereby influencing the bacterial, acidobacterial, and fungal diversity and community structure. Once the soil microbial community has been altered by human activity, it might be difficult to restore it to its original state. These findings highlight the importance of effectively maintaining the diversity of soil bacterial, Acidobacterial, and fungal communities despite land use change in order to sustain a microbial community diversity and ecosystem function.
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Affiliation(s)
- Xin Sui
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China.,Institute of Nature of Ecology, Heilongjiang Academy of Science, Harbin, China
| | - Rongtao Zhang
- Institute of Nature of Ecology, Heilongjiang Academy of Science, Harbin, China
| | - Beat Frey
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Libin Yang
- Institute of Nature of Ecology, Heilongjiang Academy of Science, Harbin, China
| | - Mai-He Li
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland. .,Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, 130024, China.
| | - Hongwei Ni
- Institute of Nature of Ecology, Heilongjiang Academy of Science, Harbin, China.
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42
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Iliev I, Marhova M, Kostadinova S, Gochev V, Tsankova M, Ivanova A, Yahubyan G, Baev V. Metagenomic analysis of the microbial community structure in protected wetlands in the Maritza River Basin. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1697364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Ivan Iliev
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Mariana Marhova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Sonya Kostadinova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Velizar Gochev
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Marinela Tsankova
- Faculty of Biology, Department of Biochemistry and Microbiology, University of Plovdiv, Plovdiv, Bulgaria
| | - Angelina Ivanova
- Institute of Fisheries and Aquaculture, Agriculture Academy, Plovdiv, Bulgaria
| | - Galina Yahubyan
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
| | - Vesselin Baev
- Faculty of Biology, Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv, Bulgaria
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Petersen IAB, Meyer KM, Bohannan BJM. Meta-Analysis Reveals Consistent Bacterial Responses to Land Use Change Across the Tropics. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00391] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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44
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Lathifah AN, Guo Y, Sakagami N, Suda W, Higuchi M, Nishizawa T, Prijambada ID, Ohta H. Comparative Characterization of Bacterial Communities in Moss-Covered and Unvegetated Volcanic Deposits of Mount Merapi, Indonesia. Microbes Environ 2019; 34:268-277. [PMID: 31327812 PMCID: PMC6759343 DOI: 10.1264/jsme2.me19041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/15/2019] [Indexed: 01/30/2023] Open
Abstract
Microbial colonization, followed by succession, on newly exposed volcanic substrates represents the beginning of the development of an early ecosystem. During early succession, colonization by mosses or plants significantly alters the pioneer microbial community composition through the photosynthetic carbon input. To provide further insights into this process, we investigated the three-year-old volcanic deposits of Mount Merapi, Indonesia. Samples were collected from unvegetated (BRD) and moss-covered (BRUD) sites. Forest site soil (FRS) near the volcanic deposit-covered area was also collected for reference. An analysis of BRD and BRUD revealed high culturable cell densities (1.7-8.5×105 CFU g-1) despite their low total C (<0.01%). FRS possessed high CFU (3×106 g-1); however, its relative value per unit of total C (2.6%) was lower than that of the deposit samples. Based on the tag pyrosequencing of 16S rRNA genes, the BRD bacterial community was characterized by a higher number of betaproteobacterial families (or genus), represented by chemolithotrophic Methylophilaceae, Leptothrix, and Sulfuricellaceae. In contrast, BRUD was predominated by different betaproteobacterial families, such as Oxalobacteraceae, Comamonadaceae, and Rhodocyclaceae. Some bacterial (Oxalobacteraceae) sequences were phylogenetically related to those of known moss-associated bacteria. Within the FRS community, Proteobacteria was the most abundant phylum, followed by Acidobacteria, whereas Burkholderiaceae was the most dominant bacterial family within FRS. These results suggest that an inter-family succession of Betaproteobacteria occurred in response to colonization by mosses, followed by plants.
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Affiliation(s)
- Annisa N. Lathifah
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology3–5–8 Saiwai-cho, Fuchu-shi, Tokyo 183–8509Japan
- Ibaraki University College of Agriculture3–21–1 Chuo, Ami-machi, Ibaraki 300–0393Japan
| | - Yong Guo
- Ibaraki University College of Agriculture3–21–1 Chuo, Ami-machi, Ibaraki 300–0393Japan
| | - Nobuo Sakagami
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology3–5–8 Saiwai-cho, Fuchu-shi, Tokyo 183–8509Japan
- Ibaraki University College of Agriculture3–21–1 Chuo, Ami-machi, Ibaraki 300–0393Japan
| | - Wataru Suda
- Department of Computational Biology, Graduate School of Frontier Science, The University of TokyoKashiwaJapan
| | - Masanobu Higuchi
- Department of Botany, National Museum of Nature and Science4–1–1, Amakubo, IbarakiJapan
| | - Tomoyasu Nishizawa
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology3–5–8 Saiwai-cho, Fuchu-shi, Tokyo 183–8509Japan
- Ibaraki University College of Agriculture3–21–1 Chuo, Ami-machi, Ibaraki 300–0393Japan
| | - Irfan D. Prijambada
- Graduate School of Biotechnology, University of Gadjah MadaYogyakartaIndonesia
| | - Hiroyuki Ohta
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology3–5–8 Saiwai-cho, Fuchu-shi, Tokyo 183–8509Japan
- Ibaraki University College of Agriculture3–21–1 Chuo, Ami-machi, Ibaraki 300–0393Japan
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Meyer KM, Petersen IAB, Tobi E, Korte L, Bohannan BJM. Use of RNA and DNA to Identify Mechanisms of Bacterial Community Homogenization. Front Microbiol 2019; 10:2066. [PMID: 31572314 PMCID: PMC6749020 DOI: 10.3389/fmicb.2019.02066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022] Open
Abstract
Biotic homogenization, i.e., the increase in community similarity through time or space, is a commonly observed response following conversion of native ecosystems to agriculture, but our understanding of the ecological mechanisms underlying this process is limited for bacterial communities. Identifying mechanisms of bacterial community homogenization following rapid environmental change may be complicated by the fact only a minority of taxa is active at any time. Here we used RNA- and DNA-based metabarcoding to distinguish putatively active taxa in the bacterial community from inactive taxa. We asked how soil bacterial communities respond to land use change following a rapid transition from rainforest to agriculture in the Congo Basin using a chronosequence that spans from roughly 1 week following slash-and-burn to an active plantation roughly 1.5 years post-conversion. Our results indicate that the magnitude of community homogenization is larger in the RNA-inferred community than the DNA-inferred perspective. We show that as the soil environment changes, the RNA-inferred community structure tracks environmental variation and loses spatial structure. The DNA-inferred community does not respond to environmental variability to the same degree, and is instead homogenized by a subset of taxa that is shared between forest and conversion sites. Our results suggest that complementing DNA-based surveys with RNA can provide insights into the way bacterial communities respond to environmental change.
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Affiliation(s)
- Kyle M. Meyer
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Ian A. B. Petersen
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Elie Tobi
- Smithsonian Institute, Gabon Biodiversity Program, Gamba, Gabon
| | - Lisa Korte
- Smithsonian Institute, Gabon Biodiversity Program, Gamba, Gabon
| | - Brendan J. M. Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
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46
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Zheng Q, Hu Y, Zhang S, Noll L, Böckle T, Dietrich M, Herbold CW, Eichorst SA, Woebken D, Richter A, Wanek W. Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity. SOIL BIOLOGY & BIOCHEMISTRY 2019; 136:107521. [PMID: 31700196 PMCID: PMC6837881 DOI: 10.1016/j.soilbio.2019.107521] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Microorganisms are critical in mediating carbon (C) and nitrogen (N) cycling processes in soils. Yet, it has long been debated whether the processes underlying biogeochemical cycles are affected by the composition and diversity of the soil microbial community or not. The composition and diversity of soil microbial communities can be influenced by various environmental factors, which in turn are known to impact biogeochemical processes. The objectives of this study were to test effects of multiple edaphic drivers individually and represented as the multivariate soil environment interacting with microbial community composition and diversity, and concomitantly on multiple soil functions (i.e. soil enzyme activities, soil C and N processes). We employed high-throughput sequencing (Illumina MiSeq) to analyze bacterial/archaeal and fungal community composition by targeting the 16S rRNA gene and the ITS1 region of soils collected from three land uses (cropland, grassland and forest) deriving from two bedrock forms (silicate and limestone). Based on this data set we explored single and combined effects of edaphic variables on soil microbial community structure and diversity, as well as on soil enzyme activities and several soil C and N processes. We found that both bacterial/archaeal and fungal communities were shaped by the same edaphic factors, with most single edaphic variables and the combined soil environment representation exerting stronger effects on bacterial/archaeal communities than on fungal communities, as demonstrated by (partial) Mantel tests. We also found similar edaphic controls on the bacterial/archaeal/fungal richness and diversity. Soil C processes were only directly affected by the soil environment but not affected by microbial community composition. In contrast, soil N processes were significantly related to bacterial/archaeal community composition and bacterial/archaeal/fungal richness/diversity but not directly affected by the soil environment. This indicates direct control of the soil environment on soil C processes and indirect control of the soil environment on soil N processes by structuring the microbial communities. The study further highlights the importance of edaphic drivers and microbial communities (i.e. composition and diversity) on important soil C and N processes.
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Affiliation(s)
- Qing Zheng
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Yuntao Hu
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shasha Zhang
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Lisa Noll
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Theresa Böckle
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Marlies Dietrich
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Craig W. Herbold
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Stephanie A. Eichorst
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Dagmar Woebken
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Althanstrasse 14, 1090 Vienna, Austria
| | - Andreas Richter
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
| | - Wolfgang Wanek
- University of Vienna, Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstrasse 14, 1090 Vienna, Austria
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47
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de Chaves MG, Silva GGZ, Rossetto R, Edwards RA, Tsai SM, Navarrete AA. Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers. Front Microbiol 2019; 10:1680. [PMID: 31417506 PMCID: PMC6682628 DOI: 10.3389/fmicb.2019.01680] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/08/2019] [Indexed: 11/21/2022] Open
Abstract
Acidobacteria is a predominant bacterial phylum in tropical agricultural soils, including sugarcane cultivated soils. The increased need for fertilizers due to the expansion of sugarcane production is a threat to the ability of the soil to maintain its potential for self-regulation in the long term, in witch carbon degradation has essential role. In this study, a culture-independent approach based on high-throughput DNA sequencing and microarray technology was used to perform taxonomic and functional profiling of the Acidobacteria community in a tropical soil under sugarcane (Saccharum spp.) that was supplemented with nitrogen (N) combined with vinasse. These analyses were conducted to identify the subgroup-level responses to chemical changes and the carbon (C) degradation potential of the different Acidobacteria subgroups. Eighteen Acidobacteria subgroups from a total of 26 phylogenetically distinct subgroups were detected based on high-throughput DNA sequencing, and 16 gene families associated with C degradation were quantified using Acidobacteria-derived DNA microarray probes. The subgroups Gp13 and Gp18 presented the most positive correlations with the gene families associated with C degradation, especially those involved in hemicellulose degradation. However, both subgroups presented low abundance in the treatment containing vinasse. In turn, the Gp4 subgroup was the most abundant in the treatment that received vinasse, but did not present positive correlations with the gene families for C degradation analyzed in this study. The metabolic potential for C degradation of the different Acidobacteria subgroups in sugarcane soil amended with N and vinasse can be driven in part through the increase in soil nutrient availability, especially calcium (Ca), magnesium (Mg), potassium (K), aluminum (Al), boron (B) and zinc (Zn). This soil management practice reduces the abundance of Acidobacteria subgroups, including those potentially involved with C degradation in this agricultural soil.
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Affiliation(s)
- Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Raffaella Rossetto
- São Paulo's Agency for Agribusiness Technology APTA-SAA, Piracicaba, Brazil
| | - Robert Alan Edwards
- Computational Science Research Center, San Diego State University, San Diego, CA, United States
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Acacio Aparecido Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil.,Department of Environmental Sciences, Federal University of São Carlos, Sorocaba, Brazil
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48
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A time travel story: metagenomic analyses decipher the unknown geographical shift and the storage history of possibly smuggled antique marble statues. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-1446-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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49
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Berkelmann D, Schneider D, Engelhaupt M, Heinemann M, Christel S, Wijayanti M, Meryandini A, Daniel R. How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities. Front Microbiol 2018; 9:2381. [PMID: 30364106 PMCID: PMC6191527 DOI: 10.3389/fmicb.2018.02381] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Palm oil production in Indonesia increased constantly over the last decades, which led to massive deforestation, especially on Sumatra island. The ongoing conversion of rainforest to agricultural systems results in high biodiversity loss. Here, we present the first RNA-based study on the effects of rainforest transformation to rubber and oil palm plantations in Indonesia for the active soil bacterial communities. For this purpose, bacterial communities of three different converted systems (jungle rubber, rubber plantation, and oil palm plantation) were studied in two landscapes with rainforest as reference by RT-PCR amplicon-based analysis of 16S rRNA gene transcripts. Active soil bacterial communities were dominated by Frankiales (Actinobacteria), subgroup 2 of the Acidobacteria and Alphaproteobacteria (mainly Rhizobiales and Rhodospirillales). Community composition differed significantly between the converted land use systems and rainforest reference sites. Alphaproteobacteria decreased significantly in oil palm samples compared to rainforest samples. In contrast, relative abundances of taxa within the Acidobacteria increased. Most important abiotic drivers for shaping soil bacterial communities were pH, calcium concentration, base saturation and C:N ratio. Indicator species analysis showed distinct association patterns for the analyzed land use systems. Nitrogen-fixing taxa including members of Rhizobiales and Rhodospirillales were associated with rainforest soils while nitrifiers and heat-resistant taxa including members of Actinobacteria were associated with oil palm soils. Predicted metabolic profiles revealed that the relative abundances of genes associated with fixation of nitrogen significantly decreased in plantation soils. Furthermore, predicted gene abundances regarding motility, competition or gene transfer ability indicated rainforest conversion-induced changes as well.
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Affiliation(s)
- Dirk Berkelmann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Martin Engelhaupt
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Melanie Heinemann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Stephan Christel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Marini Wijayanti
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
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50
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Song M, Peng W, Zeng F, Du H, Peng Q, Xu Q, Chen L, Zhang F. Spatial Patterns and Drivers of Microbial Taxa in a Karst Broadleaf Forest. Front Microbiol 2018; 9:1691. [PMID: 30093895 PMCID: PMC6070632 DOI: 10.3389/fmicb.2018.01691] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/06/2018] [Indexed: 11/13/2022] Open
Abstract
Spatial patterns and drivers of soil microbial communities have not yet been well documented. Here, we used geostatistical modeling and Illumina sequencing of 16S rRNA genes to explore how the main microbial taxa at the phyla level are spatially distributed in a 25-ha karst broadleaf forest in southwest China. Proteobacteria, dominated by Alpha- and Deltaproteobacteria, was the most abundant phylum (34.51%) in the karst forest soils. Other dominating phyla were Actinobacteria (30.73%), and Acidobacteria (12.24%). Soil microbial taxa showed spatial dependence with an autocorrelation range of 44.4-883.0 m, most of them within the scope of the study plots (500 m). An increasing trend was observed for Alphaproteobacteria, Deltaproteobacteria, and Chloroflexi from north to south in the study area, but an opposite trend for Actinobacteria, Acidobacteira, and Firmicutes was observed. Thaumarchaeota, Bacteroidetes, Gemmatimonadetes, and Verrucomicrobia had patchy patterns, Nitrospirae had a unimodal pattern, and Latescibacteria had an intermittent pattern with low and high value strips. Location, soil total phosphorus, elevation, and plant density were significantly correlated with main soil bacterial taxa in the karst forest. Moreover, the total variation in soil microbial communities better explained by spatial factors than environmental variables. Furthermore, a large part of variation (76.8%) was unexplained in the study. Therefore, our results suggested that dispersal limitation was the primary driver of spatial pattern of soil microbial taxa in broadleaved forest in karst areas, and other environmental variables (i.e., soil porosity and temperature) should be taken into consideration.
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Affiliation(s)
- Min Song
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Agricultural College, Hunan Agricultural University, Changsha, China
| | - Wanxia Peng
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Fuping Zeng
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Hu Du
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Qin Peng
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Qingguo Xu
- Agricultural College, Hunan Agricultural University, Changsha, China
| | - Li Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Fang Zhang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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