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Niu Y, Kang E, Li Y, Zhang X, Yan Z, Li M, Yan L, Zhang K, Wang X, Yang A, Yu X, Kang X, Cui X. Non-flooding conditions caused by water table drawdown alter microbial network complexity and decrease multifunctionality in alpine wetland soils. ENVIRONMENTAL RESEARCH 2024; 254:119152. [PMID: 38754612 DOI: 10.1016/j.envres.2024.119152] [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: 03/15/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/18/2024]
Abstract
Several soil functions of alpine wetland depend on microbial communities, including carbon storage and nutrient cycling, and soil microbes are highly sensitive to hydrological conditions. Wetland degradation is often accompanied by a decline in water table. With the water table drawdown, the effects of microbial network complexity on various soil functions remain insufficiently understood. In this research, we quantified soil multifunctionality of flooded and non-flooded sites in the Lalu Wetland on the Tibetan Plateau. We employed high-throughput sequencing to investigate the microbial community responses to water table depth changes, as well as the relationships between microbial network properties and soil multifunctionality. Our findings revealed a substantial reduction in soil multifunctionality at both surface and subsurface soil layers (0-20 cm and 20-40 cm) in non-flooded sites compared to flooded sites. The α-diversity of bacteria in the surface soil of non-flooded sites was significantly lower than that in flooded sites. Microbial network properties (including the number of nodes, number of edges, average degree, density, and modularity of co-occurrence networks) exhibited significant correlations with soil multifunctionality. This study underscores the adverse impact of non-flooded conditions resulting from water table drawdown on soil multifunctionality in alpine wetland soils, driven by alterations in microbial community structure. Additionally, we identified soil pH and moisture content as pivotal abiotic factors influencing soil multifunctionality, with microbial network complexity emerging as a valuable predictor of multifunctionality.
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Affiliation(s)
- Yuechuan Niu
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Enze Kang
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yong Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Xiaodong Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Zhongqing Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Meng Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Liang Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Kerou Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Xiaodong Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ao Yang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Xiaoshun Yu
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China
| | - Xiaoming Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, China.
| | - Xiaoyong Cui
- University of Chinese Academy of Sciences, Beijing 100049, China.
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Picariello E, De Nicola F. Recover of Soil Microbial Community Functions in Beech and Turkey Oak Forests After Coppicing Interventions. MICROBIAL ECOLOGY 2024; 87:86. [PMID: 38940921 PMCID: PMC11213729 DOI: 10.1007/s00248-024-02402-2] [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: 02/26/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.
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Affiliation(s)
- Enrica Picariello
- Department of Sciences and Technologies, University of Sannio, 82100, Benevento, Italy.
| | - Flavia De Nicola
- Department of Sciences and Technologies, University of Sannio, 82100, Benevento, Italy
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Błońska E, Ważny R, Górski A, Lasota J. Decomposing benefits: Examining the impact of beech deadwood on soil properties and microbial diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172774. [PMID: 38685423 DOI: 10.1016/j.scitotenv.2024.172774] [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: 12/03/2023] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/02/2024]
Abstract
Deadwood is an important element of forest ecosystems that affects many of its components, including the soil environment. Our research is an attempt to determine the role of decaying wood in shaping the properties of forest soils in mountain ecosystems. The aim of our research was to present the influence of beech deadwood on physicochemical properties and microbiological diversity of soils. The research was carried out in the Baba Góra Massif at its northern exposure. The research plots were established in the altitude gradient at 600, 800 and 1000 m above sea level. On each plot, samples were taken from decaying wood, from the soil directly under the decaying log, and a soil sample 1 m from the log as a control. We determined the basic properties of the samples, that is pH, C and N concentration and lignin content. The enzymatic activity and additionally, the taxonomic composition of soil bacterial and fungal communities was determined in the collected samples. Our research indicates the important role of decaying beech wood in shaping the properties of forest soils. We noted a positive effect of decaying wood on the properties of the tested soils. Soils affected by deadwood were characterized by significantly higher pH, C and N concentrations compared to control soils, regardless of their location in the altitude gradient. Additionally, we found that soils affected by decaying wood are characterized by a different composition of microorganisms regardless of their location in the altitude gradient. In control soil the fungal and bacterial alpha diversity were lowest compared with the deadwood and soil under the influence of deadwood. Our results may have practical applications in the management of forest ecosystems. The presented results indicate the possibility of leaving deadwood in order to improve its basic physicochemical properties and increase microbial diversity.
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Affiliation(s)
- Ewa Błońska
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture in Krakow, 29 Listopada 46 Str., 31-425 Kraków, Poland.
| | - Rafał Ważny
- Małopolska Centre of Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7a, 30-387 Kraków, Poland
| | - Adam Górski
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture in Krakow, 29 Listopada 46 Str., 31-425 Kraków, Poland
| | - Jarosław Lasota
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture in Krakow, 29 Listopada 46 Str., 31-425 Kraków, Poland
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Cho I, Lee SY, Cho KS. Enhancement of the germination and growth of Panicum miliaceum and Brassica juncea in Cd- and Zn-contaminated soil inoculated with heavy-metal-tolerant Leifsonia sp. ZP3. World J Microbiol Biotechnol 2024; 40:245. [PMID: 38884883 DOI: 10.1007/s11274-024-04053-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
The addition of plant-growth-promoting bacteria (PGPB) to heavy-metal-contaminated soils can significantly improve plant growth and productivity. This study isolated heavy-metal-tolerant bacteria with growth-promoting traits and investigated their inoculation effects on the germination rates and growth of millet (Panicum miliaceum) and mustard (Brassica juncea) in Cd- and Zn-contaminated soil. Leifsonia sp. ZP3, which is resistant to Cd (0.5 mM) and Zn (1 mM), was isolated from forest soil. The ZP3 strain exhibited plant-growth-promoting activity, including indole-3-acetic acid production, phosphate solubilization, catalase activity, and 2,2-diphenyl-1-picrylhydrazyl radical scavenging. In soil contaminated with low concentrations of Cd (0.232 ± 0.006 mM) and Zn (6.376 ± 0.256 mM), ZP3 inoculation significantly increased the germination rates of millet and mustard 8.35- and 31.60-fold, respectively, compared to the non-inoculated control group, while the shoot and root lengths of millet increased 1.77- and 4.44-fold (p < 0.05). The chlorophyll content and seedling vigor index were also 4.40 and 18.78 times higher in the ZP3-treated group than in the control group (p < 0.05). The shoot length of mustard increased 1.89-fold, and the seedling vigor index improved 53.11-fold with the addition of ZP3 to the contaminated soil (p < 0.05). In soil contaminated with high concentrations of Cd and Zn (0.327 ± 0.016 and 8.448 ± 0.250 mM, respectively), ZP3 inoculation led to a 1.98-fold increase in the shoot length and a 2.07-fold improvement in the seedling vigor index compared to the control (p < 0.05). The heavy-metal-tolerant bacterium ZP3 isolated in this study thus represents a promising microbial resource for improving the efficiency of phytoremediation in Cd- and Zn-contaminated soil.
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Affiliation(s)
- Ian Cho
- Department of Environmental Science and Engineering, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea
| | - Soo Yeon Lee
- Department of Environmental Science and Engineering, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea
| | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea.
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Guo P, Li S, Zhu J, Lu Q. Variation in soil bacterial community characteristics inside and outside the West Ordos National Nature Reserve, northern China. Front Microbiol 2024; 15:1404848. [PMID: 38919497 PMCID: PMC11196814 DOI: 10.3389/fmicb.2024.1404848] [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: 03/21/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024] Open
Abstract
Nature reserves are crucial for protecting biological habitats and maintaining biodiversity. Soil bacterial community plays an irreplaceable role in the structure and function of ecosystem. However, the impact of nature reserves on soil bacterial communities is still unclear. To explore the effects of desert grassland nature reserve management on soil microbial communities, we compared the differences in soil bacterial community composition, α-diversity and community structure inside and outside a desert grassland nature reserve, and explored the correlation between soil bacterial communities and plant biomass and soil chemical index. We found that (1) the relative abundance of Acidobacteriota is highest in the soil both inside and outside the nature reserve in shrub grassland; (2) the Chao1 index of soil bacterial communities in the core protected zone and general control zone of the reserve was significantly higher than that outside the reserve (p < 0.05) in the shrub grassland. Similarly, in the herbaceous grassland, the Shannon index of soil bacterial communities was significantly higher in the core protected zone of the reserve than that outside the reserve (p < 0.05). (3) While we found no significant difference in soil bacterial community structure between inside and outside the reserve in the shrub grassland, we found that the soil bacterial community structure in the core protected zone was significantly different from that outside the reserve in the herbaceous grassland (p < 0.05); (4) we also found that higher plant productivity and soil nutrients promoted most soil dominant bacterial phyla, while higher soil pH and salinity inhibited most soil dominant bacterial phyla. Our findings thus help better understand the influencing factors of and the mechanisms behind variation in soil bacterial communities inside and outside desert grassland nature reserves.
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Affiliation(s)
- Pu Guo
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
| | - Shuai Li
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou, China
| | - Jinlei Zhu
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
| | - Qi Lu
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
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Bereczki K, Tóth EG, Szili-Kovács T, Megyes M, Korponai K, Lados BB, Illés G, Benke A, Márialigeti K. Soil Parameters and Forest Structure Commonly Form the Microbiome Composition and Activity of Topsoil Layers in Planted Forests. Microorganisms 2024; 12:1162. [PMID: 38930544 PMCID: PMC11205539 DOI: 10.3390/microorganisms12061162] [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: 05/10/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Soil bacterial communities play a remarkable role in nutrient cycling, significantly affecting soil organic material content, soil fertility, and, in an indirect way, plant succession processes. Conversely, vegetation type influences microbial soil life. The present study compared the bacterial microbiome composition, diversity and catabolic activity profile of topsoil samples collected under three different forest types (a twice-coppiced black locust stand, a young, naturally reforested, and a middle-aged mixed pedunculate oak stand) planted on former arable land in the early 20th century. Diversity indices determined during 16S ribosomal RNA sequencing-based metagenome analysis indicated that the black locust stand had the highest soil bacterial community diversity. At the phylum level, Acidobacteriota, Actinobacteriota, Proteobacteria, Verrucomicrobiota, Bacteroidota, and Gemmatimonadota were the most abundant taxa in the forest soils. Concerning soil parameters, redundancy analysis revealed that pH had the highest impact on bacterial community structure and pH, and soil organic carbon content on the samples' respiration patterns. As for catabolic activity, the recently clearcut oak forest showed the lowest substrate-induced respiration, and citrate was the main driver for the inter-stand variability of microbial activity. Our results confirm that soil parameters and forest type influence the composition and functioning of the soil bacterial microbiome.
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Affiliation(s)
- Katalin Bereczki
- Doctoral School of Environmental Sciences, Eötvös Loránd University, 1117 Budapest, Hungary;
- Department of Forest Management and Ecology, Forest Research Institute, University of Sopron, 9600 Sárvár, Hungary;
| | - Endre György Tóth
- National Coalition of Independent Scholars (NCIS), Brattleboro, VT 05301, USA;
| | - Tibor Szili-Kovács
- Institute for Soil Sciences, Centre for Agricultural Research, 1022 Budapest, Hungary;
| | - Melinda Megyes
- Doctoral School of Environmental Sciences, Eötvös Loránd University, 1117 Budapest, Hungary;
| | - Kristóf Korponai
- Department of Plant Molecular Biology, Agricultural Institute, Centre for Agricultural Research, 2462 Martonvásár, Hungary;
| | - Botond Boldizsár Lados
- Department of Forestry Breeding, Forest Research Institute, University of Sopron, 9600 Sárvár, Hungary; (B.B.L.); (A.B.)
| | - Gábor Illés
- Department of Forest Management and Ecology, Forest Research Institute, University of Sopron, 9600 Sárvár, Hungary;
| | - Attila Benke
- Department of Forestry Breeding, Forest Research Institute, University of Sopron, 9600 Sárvár, Hungary; (B.B.L.); (A.B.)
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, 1117 Budapest, Hungary;
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Benalcazar P, Seuradge B, Diochon AC, Kolka RK, Phillips LA. Conversion of boreal forests to agricultural systems: soil microbial responses along a land-conversion chronosequence. ENVIRONMENTAL MICROBIOME 2024; 19:32. [PMID: 38734653 PMCID: PMC11088160 DOI: 10.1186/s40793-024-00576-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Boreal regions are warming at more than double the global average, creating opportunities for the northward expansion of agriculture. Expanding agricultural production in these regions will involve the conversion of boreal forests to agricultural fields, with cumulative impacts on soil microbial communities and associated biogeochemical cycling processes. Understanding the magnitude or rate of change that will occur with these biological processes will provide information that will enable these regions to be developed in a more sustainable manner, including managing carbon and nitrogen losses. This study, based in the southern boreal region of Canada where agricultural expansion has been occurring for decades, used a paired forest-adjacent agricultural field approach to quantify how soil microbial communities and functions were altered at three different stages post-conversion (< 10, > 10 and < 50, and > 50 years). Soil microbial functional capacity was assessed by quantitative PCR of genes associated with carbon (C), nitrogen, and phosphorous (P) cycling; microbial taxonomic diversity and community structure was assessed by amplicon sequencing. RESULTS Fungal alpha diversity did not change, but communities shifted from Basidiomycota to Ascomycota dominant within the first decade. Bacterial alpha diversity increased, with Gemmatimonadota groups generally increasing and Actinomycetota groups generally decreasing in agricultural soils. These altered communities led to altered functional capacity. Functional genes associated with nitrification and low molecular weight C cycling potential increased after conversion, while those associated with organic P mineralization potential decreased. Stable increases in most N cycling functions occurred within the first decade, but C cycling functions were still changing 50 years post conversion. CONCLUSIONS Microbial communities underwent a rapid shift in the first decade, followed by several decades of slower transition until stabilizing 50 years post conversion. Understanding how the microbial communities respond at different stages post-conversion improves our ability to predict C and N losses from emerging boreal agricultural systems, and provides insight into how best to manage these soils in a way that is sustainable at the local level and within a global context.
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Affiliation(s)
- Paul Benalcazar
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON, Canada
| | - Brent Seuradge
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON, Canada
| | - Amanda C Diochon
- Department of Geology, Lakehead University, Thunder Bay, ON, Canada
| | - Randall K Kolka
- USDA Forest Services Northern Research Station, Grand Rapid, MN, 55744, USA
| | - Lori A Phillips
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON, Canada.
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Melo de Queiroz T, Valdes TA, Leitão A, Porto ALM. Bio-oxidation of progesterone by Penicillium oxalicum CBMAI 1185 and evaluation of the cytotoxic activity. Steroids 2024; 205:109392. [PMID: 38452910 DOI: 10.1016/j.steroids.2024.109392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
We report the biotransformation of progesterone 1 by whole cells of Brazilian marine-derived fungi. A preliminary screening with 12 fungi revealed that the strains Penicillium oxalicum CBMAI 1996, Mucor racemous CBMAI 847, Cladosporium sp. CBMAI 1237, Penicillium oxalicum CBMAI 1185 and Aspergillus sydowii CBMAI 935 were efficient in the biotransformation of progesterone 1 in the first days of the reaction, with conversion values ranging from 75 % to 99 %. The fungus P. oxalicum CBMAI 1185 was employed in the reactions in quintuplicate to purify and characterize the main biotransformation products of progesterone 1. The compounds testololactone 1a, 12β-hydroxyandrostenedione 1b and 1β-hydroxyandrostenedione 1c were isolated and characterized by NMR, MS, [α]D and MP. In addition, the chromatographic yield of compound 1a was determined by HPLC-PDA in the screening experiments. In this study, we show a biotransformation pathway of progesterone 1, suggesting the presence of several enzymes such as Baeyer-Villiger monooxygenases, dehydrogenases and cytochrome P450 monooxygenases in the fungus P. oxalicum CBMAI 1185. In summary, the results obtained in this study contribute to the synthetic area and have environmental importance, since the marine-derived fungi can be employed in the biodegradation of steroids present in wastewater and the environment. The cytotoxic results demonstrate that the biodegradation products were inactive against the cell lines, in contrast to progesterone.
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Affiliation(s)
- Thayane Melo de Queiroz
- Laboratório de Química Orgânica e Biocatálise, Instituto de Química de São Carlos, Universidade de São Paulo, Av. João Dagnone, 1100, Química Ambiental "Edifício Prof. Douglas Wagner Franco", Santa Angelina, 13563-120 São Carlos, SP, Brazil
| | - Talita A Valdes
- Medicinal & Biological Chemistry Group, Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-Carlense, 400, 13566-590, São Carlos, SP, Brazil
| | - Andrei Leitão
- Medicinal & Biological Chemistry Group, Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-Carlense, 400, 13566-590, São Carlos, SP, Brazil
| | - André L M Porto
- Laboratório de Química Orgânica e Biocatálise, Instituto de Química de São Carlos, Universidade de São Paulo, Av. João Dagnone, 1100, Química Ambiental "Edifício Prof. Douglas Wagner Franco", Santa Angelina, 13563-120 São Carlos, SP, Brazil.
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Lopez JG, Hein Y, Erez A. Grow now, pay later: When should a bacterium go into debt? Proc Natl Acad Sci U S A 2024; 121:e2314900121. [PMID: 38588417 PMCID: PMC11032434 DOI: 10.1073/pnas.2314900121] [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: 08/28/2023] [Accepted: 03/03/2024] [Indexed: 04/10/2024] Open
Abstract
Microbes grow in a wide variety of environments and must balance growth and stress resistance. Despite the prevalence of such trade-offs, understanding of their role in nonsteady environments is limited. In this study, we introduce a mathematical model of "growth debt," where microbes grow rapidly initially, paying later with slower growth or heightened mortality. We first compare our model to a classical chemostat experiment, validating our proposed dynamics and quantifying Escherichia coli's stress resistance dynamics. Extending the chemostat theory to include serial-dilution cultures, we derive phase diagrams for the persistence of "debtor" microbes. We find that debtors cannot coexist with nondebtors if "payment" is increased mortality but can coexist if it lowers enzyme affinity. Surprisingly, weak noise considerably extends the persistence of resistance elements, pertinent for antibiotic resistance management. Our microbial debt theory, broadly applicable across many environments, bridges the gap between chemostat and serial dilution systems.
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Affiliation(s)
- Jaime G. Lopez
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Racah Institute of Physics, The Hebrew University, Jerusalem9190401, Israel
- Department of Applied Physics, Stanford University, Stanford, CA94305
| | - Yaïr Hein
- Institute for Theoretical Physics, Utrecht University, Utrecht3584 CC, Netherlands
| | - Amir Erez
- Racah Institute of Physics, The Hebrew University, Jerusalem9190401, Israel
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Silva DEO, Costa RM, Campos JR, Rocha SMB, de Araujo Pereira AP, Melo VMM, Oliveira FAS, de Alcantara Neto F, Mendes LW, Araujo ASF. Short-term restoration practices change the bacterial community in degraded soil from the Brazilian semiarid. Sci Rep 2024; 14:6845. [PMID: 38514851 PMCID: PMC10957980 DOI: 10.1038/s41598-024-57690-y] [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: 10/16/2023] [Accepted: 03/20/2024] [Indexed: 03/23/2024] Open
Abstract
Land degradation by deforestation adversely impacts soil properties, and long-term restoration practices have been reported to potentially reverse these effects, particularly on soil microorganisms. However, there is limited knowledge regarding the short-term effects of restoration on the soil bacterial community in semiarid areas. This study evaluates the bacterial community in soils experiencing degradation (due to slash-and-burn deforestation) and restoration (utilizing stone cordons and revegetation), in comparison to a native soil in the Brazilian semiarid region. Three areas were selected: (a) under degradation; (b) undergoing short-term restoration; and (c) a native area, and the bacterial community was assessed using 16S rRNA sequencing on soil samples collected during both dry and rainy seasons. The dry and rainy seasons exhibited distinct bacterial patterns, and native sites differed from degraded and restoration sites. Chloroflexi and Proteobacteria phyla exhibited higher prevalence in degraded and restoration sites, respectively, while Acidobacteria and Actinobacteria were more abundant in sites undergoing restoration compared to degraded sites. Microbial connections varied across sites and seasons, with an increase in nodes observed in the native site during the dry season, more edges and positive connections in the restoration site, and a higher occurrence of negative connections in the degradation site during the rainy season. Niche occupancy analysis revealed that degradation favored specialists over generalists, whereas restoration exhibited a higher prevalence of generalists compared to native sites. Specifically, degraded sites showed a higher abundance of specialists in contrast to restoration sites. This study reveals that land degradation impacts the soil bacterial community, leading to differences between native and degraded sites. Restoring the soil over a short period alters the status of the bacterial community in degraded soil, fostering an increase in generalist microbes that contribute to enhanced soil stability.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil
| | - Ademir Sergio Ferreira Araujo
- Soil Microbial Ecology Group, Federal University of Piauí, Teresina, PI, Brazil.
- Soil Quality Lab., Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil.
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Liu Y, Wang H, Tan X, Fu S, Liu D, Shen W. Increased precipitation alters the effects of nitrogen deposition on soil bacterial and fungal communities in a temperate forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170017. [PMID: 38219995 DOI: 10.1016/j.scitotenv.2024.170017] [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: 11/18/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/16/2024]
Abstract
Anthropogenic nitrogen (N) deposition and increased precipitation are known to alter soil microbial communities. However, the combined effects of elevated N deposition and increased precipitation on soil microbial community dynamics and co-occurrence networks in temperate forests remain elusive. In this study, we conducted a field manipulation experiment by applying N solution and water to the forest canopy to simulate natural N deposition and increased precipitation in a temperate forest. We collected samples in the litter layer, organic soil layer, and mineral soil layer in 2018-2019 after 6-7 years of N and water treatments, and explored how elevated N deposition and increased precipitation regulate soil microbial diversity, community composition, and co-occurrence networks in different soil layers and at different sampling times. We found that the effects of N deposition and increased precipitation on soil microbial communities varied with soil layers and sampling times. Compared to the ambient environment, single canopy N addition (CN) or single canopy water addition (CW) did not affect bacterial Shannon diversity in the mineral soil layer in 2018, but the combined canopy N and water additions (CNW) decreased it in this layer at this time. CN increased fungal OTU richness in the organic and mineral soil layers in 2018; however, CW and CNW did not have an effect on it in the same layer at the same time. CW and CNW, but not CN, significantly affected bacterial and fungal community compositions in the litter layer in 2018 and in the organic soil layer in 2019. In contrast, CN, but not CW or CNW, significantly affected fungal community composition in the litter layer in 2019. CNW exhibited higher complexities of bacterial and fungal co-occurrence networks than CN and the ambient environment, indicating increased precipitation can strengthen the effect of N deposition on the complexity of bacterial and fungal co-occurrence networks. Our findings suggest that increased precipitation alters the effects of atmospheric N deposition on soil bacterial and fungal communities in this temperate forest, depending on soil layer and sampling time. Moreover, both bacterial and fungal community compositions are sensitive to increased precipitation, but the bacterial community composition is more sensitive to N deposition than the fungal community composition in the organic and mineral soil layers in this forest.
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Affiliation(s)
- Yang Liu
- Sichuan Provincial Forest and Grassland Key Laboratory of Alpine Grassland Conservation and Utilization of Tibetan Plateau, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Hang Wang
- National Plateau Wetlands Research Center/Wetlands College, Southwest Forestry University, Kunming, China.
| | - Xiangping Tan
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Shenglei Fu
- Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions, Ministry of Education, College of Environment and Planning, Henan University, Kaifeng, China
| | - Dan Liu
- Sichuan Provincial Forest and Grassland Key Laboratory of Alpine Grassland Conservation and Utilization of Tibetan Plateau, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Weijun Shen
- Guangxi Key Laboratory of Forest Ecology and Conservation, State Key Laboratory for Conservation and Utilization of Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi, China.
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12
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Hopkins AJM, Brace AJ, Bruce JL, Hyde J, Fontaine JB, Walden L, Veber W, Ruthrof KX. Drought legacy interacts with wildfire to alter soil microbial communities in a Mediterranean climate-type forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170111. [PMID: 38232837 DOI: 10.1016/j.scitotenv.2024.170111] [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: 06/22/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Mediterranean forest ecosystems will be increasingly affected by hotter drought and more frequent and severe wildfire events in the future. However, little is known about the longer-term responses of these forests to multiple disturbances and the forests' capacity to maintain ecosystem function. This is particularly so for below-ground organisms, which have received less attention than those above-ground, despite their essential contributions to forest function. We investigated rhizosphere microbial communities in a resprouting Eucalyptus marginata forest, southwestern Australia, that had experienced a severe wildfire four years previously, and a hotter drought eight years previously. Our aim was to understand how microbial communities are affected over longer-term trajectories by hotter drought and wildfire, singularly, and in combination. Fungal and bacterial DNA was extracted from soil samples, amplified, and subjected to high throughput sequencing. Richness, diversity, composition, and putative functional groups were then examined. We found a monotonic decrease in fungal, but not bacterial, richness and diversity with increasing disturbance with the greatest changes resulting from the combination of drought and wildfire. Overall fungal and bacterial community composition reflected a stronger effect of fire than drought, but the combination of both produced the greatest number of indicator taxa for fungi, and a significant negative effect on the abundance of several fungal functional groups. Key mycorrhizal fungi, fungal saprotrophs and fungal pathogens were found at lower proportions in sites affected by drought plus wildfire. Wildfire had a positive effect on bacterial hydrogen and bacterial nitrogen recyclers. Fungal community composition was positively correlated with live tree height. These results suggest that microbial communities, in particular key fungal functional groups, are highly responsive to wildfire following drought. Thus, a legacy of past climate conditions such as hotter drought can be important for mediating the responses of soil microbial communities to subsequent disturbance like wildfire.
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Affiliation(s)
- A J M Hopkins
- Molecular Ecology and Evolution Group, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia.
| | - A J Brace
- Molecular Ecology and Evolution Group, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - J L Bruce
- Molecular Ecology and Evolution Group, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia
| | - J Hyde
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, WA 6151, Australia
| | - J B Fontaine
- School of Environmental and Conservation Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - L Walden
- Soil and Landscape Science, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - W Veber
- School of Environmental and Conservation Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - K X Ruthrof
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, WA 6151, Australia; School of Environmental and Conservation Sciences, Murdoch University, Murdoch, WA 6150, Australia
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13
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Schrader L, Trautner J, Tebbe CC. Identifying environmental factors affecting the microbial community composition on outdoor structural timber. Appl Microbiol Biotechnol 2024; 108:254. [PMID: 38446240 PMCID: PMC10917859 DOI: 10.1007/s00253-024-13089-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/19/2024] [Accepted: 02/25/2024] [Indexed: 03/07/2024]
Abstract
Timber wood is a building material with many positive properties. However, its susceptibility to microbial degradation is a major challenge for outdoor usage. Although many wood-degrading fungal species are known, knowledge on their prevalence and diversity causing damage to exterior structural timber is still limited. Here, we sampled 46 decaying pieces of wood from outdoor constructions in the area of Hamburg, Germany; extracted their DNA; and investigated their microbial community composition by PCR amplicon sequencing of the fungal ITS2 region and partial bacterial 16S rRNA genes. In order to establish a link between the microbial community structure and environmental factors, we analysed the influence of wood species, its C and N contents, the effect of wood-soil contact, and the importance of its immediate environment (city, forest, meadow, park, respectively). We found that fungal and bacterial community composition colonising exterior timber was similar to fungi commonly found in forest deadwood. Of all basidiomycetous sequences retrieved, some, indicative for Perenniporia meridionalis, Dacrymyces capitatus, and Dacrymyces stillatus, were more frequently associated with severe wood damage. Whilst the most important environmental factor shaping fungal and bacterial community composition was the wood species, the immediate environment was important for fungal species whilst, for the occurrence of bacterial taxa, soil contact had a high impact. No influence was tangible for variation of the C or N content. In conclusion, our study demonstrates that wood colonising fungal and bacterial communities are equally responsive in their composition to wood species, but respond differently to environmental factors. KEY POINTS: • Perenniporia meridionalis and Dacrymyces are frequently associated with wood damage • Fungal community composition on timber is affected by its surrounding environment • Bacterial community composition on structural timber is affected by soil contact.
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Affiliation(s)
- Lauritz Schrader
- Thünen Institute of Wood Research, Leuschnerstraße 91, 21031, Hamburg, Germany
| | - Jochen Trautner
- Thünen Institute of Wood Research, Leuschnerstraße 91, 21031, Hamburg, Germany
| | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Bundesallee 65, 38116, Brunswick, Germany.
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14
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Zheng F, Gu J, Lu D, Yang J, Shuai X, Li C, Chen H. Mixing with native broadleaf trees modified soil microbial communities of Cunninghamia lanceolata monocultures in South China. Front Microbiol 2024; 15:1372128. [PMID: 38505544 PMCID: PMC10949948 DOI: 10.3389/fmicb.2024.1372128] [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: 01/17/2024] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Mixing with different broadleaf trees into the monocultures of Cunninghamia lanceolata is widely adopted as an efficient transformation of the pure C. lanceolata forest. However, it is unclear how native broad-leaved trees influence the belowground ecological environment of the pure C. lanceolata culture plantation in nutrient-poor soil of South China. Herein, we aimed to investigate how a long-time mixing with native broadleaf trees shape soil microbial community of the pure C. lanceolata forest across different soil depth (0-20 cm and 20-40 cm) and to clarify relationships between the modified soil microbial community and those affected soil chemical properties. Using high-throughput sequencing technology, microbial compositions from the mixed C. lanceolata-broadleaf forest and the pure C. lanceolata forest were analyzed. Network analysis was utilized to investigate correlations among microorganisms, and network robustness was assessed by calculating network natural connectivity. Results demonstrated that the content of soil microbial biomass carbon and nitrogen, total phosphorus and pH in mixed forest stand were significantly higher than those in pure forest stand, except for available phosphorus in topsoil (0-20 cm). Simultaneously, the mixed C. lanceolata-broadleaf forest has a more homogeneous bacterial and fungal communities across different soil depth compared with the pure C. lanceolata forest, wherein the mixed forest recruited more diverse bacterial community in subsoil (20-40 cm) and reduced the diversity of fungal community in topsoil. Meanwhile, the mixed forest showed higher bacterial community stability while the pure forest showed higher fungal community stability. Moreover, bacterial communities showed significant correlations with various soil chemical indicators, whereas fungal communities exhibited correlations with only TP and pH. Therefore, the mixed C. lanceolata-broadleaf forest rely on their recruiting bacterial community to enhance and maintain the higher nutrient status of soil while the pure C. lanceolata forest rely on some specific fungi to satisfy their phosphorus requirement for survive strategy.
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Affiliation(s)
| | | | | | | | | | | | - Hongyue Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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15
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He L, Sun X, Li S, Zhou W, Yu J, Zhao G, Chen Z, Bai X, Zhang J. Depth effects on bacterial community altitudinal patterns and assembly processes in the warm-temperate montane forests of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169905. [PMID: 38190904 DOI: 10.1016/j.scitotenv.2024.169905] [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: 07/24/2023] [Revised: 10/25/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
Soil bacterial communities are essential for ecosystem function, yet their response along altitudinal gradients in different soil strata remains unclear. Understanding bacterial community co-occurrence networks and assembly patterns in mountain ecosystems is crucial for comprehending microbial ecosystem functions. We utilized Illumina MiSeq sequencing to study bacterial diversity and assembly patterns of surface and subsurface soils across a range of elevations (700 to 2100 m) on Dongling Mountain. Our results showed significant altitudinal distribution patterns concerning bacterial diversity and structure in the surface soil. The bacterial diversity exhibited a consistent decrease, while specific taxa demonstrated unique patterns along the altitudinal gradient. However, no altitudinal dependence was observed for bacterial diversity and community structure in the subsurface soil. Additionally, a shift in bacterial ecological groups is evident with changing soil depth. Copiotrophic taxa thrive in surface soils characterized by higher carbon and nutrient content, while oligotrophic taxa dominate in subsurface soils with more limited resources. Bacterial community characteristics exhibited strong correlations with soil organic carbon in both soil layers, followed by pH in the surface soil and soil moisture in the subsurface soil. With increasing depth, there is an observable increase in taxa-taxa interaction complexity and network structure within bacterial communities. The surface soil exhibits greater sensitivity to environmental perturbations, leading to increased modularity and an abundance of positive relationships in its community networks compared to the subsurface soil. Furthermore, the bacterial community at different depths was influenced by combining deterministic and stochastic processes, with stochasticity (homogenizing dispersal and undominated) decreasing and determinism (heterogeneous selection) increasing with soil depth.
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Affiliation(s)
- Libing He
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Suyan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Wenzhi Zhou
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Jiantao Yu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Guanyu Zhao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Zhe Chen
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xueting Bai
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Jinshuo Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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16
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Solanki AC, Gurjar NS, Sharma S, Wang Z, Kumar A, Solanki MK, Kumar Divvela P, Yadav K, Kashyap BK. Decoding seasonal changes: soil parameters and microbial communities in tropical dry deciduous forests. Front Microbiol 2024; 15:1258934. [PMID: 38440136 PMCID: PMC10910104 DOI: 10.3389/fmicb.2024.1258934] [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: 07/14/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024] Open
Abstract
In dry deciduous tropical forests, both seasons (winter and summer) offer habitats that are essential ecologically. How these seasonal changes affect soil properties and microbial communities is not yet fully understood. This study aimed to investigate the influence of seasonal fluctuations on soil characteristics and microbial populations. The soil moisture content dramatically increases in the summer. However, the soil pH only gradually shifts from acidic to slightly neutral. During the summer, electrical conductivity (EC) values range from 0.62 to 1.03 ds m-1, in contrast to their decline in the winter. The levels of soil macronutrients and micronutrients increase during the summer, as does the quantity of soil organic carbon (SOC). A two-way ANOVA analysis reveals limited impacts of seasonal fluctuations and specific geographic locations on the amounts of accessible nitrogen (N) and phosphorus (P). Moreover, dehydrogenase, nitrate reductase, and urease activities rise in the summer, while chitinase, protease, and acid phosphatase activities are more pronounced in the winter. The soil microbes were identified in both seasons through 16S rRNA and ITS (Internal Transcribed Spacer) gene sequencing. Results revealed Proteobacteria and Ascomycota as predominant bacterial and fungal phyla. However, Bacillus, Pseudomonas, and Burkholderia are dominant bacterial genera, and Aspergillus, Alternaria, and Trichoderma are dominant fungal genera in the forest soil samples. Dominant bacterial and fungal genera may play a role in essential ecosystem services such as soil health management and nutrient cycling. In both seasons, clear relationships exist between soil properties, including pH, moisture, iron (Fe), zinc (Zn), and microbial diversity. Enzymatic activities and microbial shift relate positively with soil parameters. This study highlights robust soil-microbial interactions that persist mainly in the top layers of tropical dry deciduous forests in the summer and winter seasons. It provides insights into the responses of soil-microbial communities to seasonal changes, advancing our understanding of ecosystem dynamics and biodiversity preservation.
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Affiliation(s)
| | - Narendra Singh Gurjar
- Department of Soil Science and Agriculture Chemistry, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, Madhya Pradesh, India
| | - Satish Sharma
- Department of Plant Pathology, B. M. College of Agriculture, Khandwa, Madhya Pradesh, India
| | - Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, China
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | | | - Kajal Yadav
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Brijendra Kumar Kashyap
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, Uttar Pradesh, India
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17
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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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18
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Bautista-Cruz A, Aquino-Bolaños T, Hernández-Canseco J, Quiñones-Aguilar EE. Cellulolytic Aerobic Bacteria Isolated from Agricultural and Forest Soils: An Overview. BIOLOGY 2024; 13:102. [PMID: 38392320 PMCID: PMC10886624 DOI: 10.3390/biology13020102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
This review provides insights into cellulolytic bacteria present in global forest and agricultural soils over a period of 11 years. It delves into the study of soil-dwelling cellulolytic bacteria and the enzymes they produce, cellulases, which are crucial in both soil formation and the carbon cycle. Forests and agricultural activities are significant contributors to the production of lignocellulosic biomass. Forest ecosystems, which are key carbon sinks, contain 20-30% cellulose in their leaf litter. Concurrently, the agricultural sector generates approximately 998 million tons of lignocellulosic waste annually. Predominant genera include Bacillus, Pseudomonas, Stenotrophomonas, and Streptomyces in forests and Bacillus, Streptomyces, Pseudomonas, and Arthrobacter in agricultural soils. Selection of cellulolytic bacteria is based on their hydrolysis ability, using artificial cellulose media and dyes like Congo red or iodine for detection. Some studies also measure cellulolytic activity in vitro. Notably, bacterial cellulose hydrolysis capability may not align with their cellulolytic enzyme production. Enzymes such as GH1, GH3, GH5, GH6, GH8, GH9, GH10, GH12, GH26, GH44, GH45, GH48, GH51, GH74, GH124, and GH148 are crucial, particularly GH48 for crystalline cellulose degradation. Conversely, bacteria with GH5 and GH9 often fail to degrade crystalline cellulose. Accurate identification of cellulolytic bacteria necessitates comprehensive genomic analysis, supplemented by additional proteomic and transcriptomic techniques. Cellulases, known for degrading cellulose, are also significant in healthcare, food, textiles, bio-washing, bleaching, paper production, ink removal, and biotechnology, emphasizing the importance of discovering novel cellulolytic strains in soil.
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Affiliation(s)
- Angélica Bautista-Cruz
- Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Teodulfo Aquino-Bolaños
- Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Jessie Hernández-Canseco
- Doctoral Programme in Conservation and Use of Natural Resources, Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Evangelina Esmeralda Quiñones-Aguilar
- Laboratorio de Fitopatología de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, El Bajío del Arenal, Zapopan 45019, Jalisco, Mexico
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19
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Jaeger ACH, Hartmann M, Conz RF, Six J, Solly EF. Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13211. [PMID: 37991154 PMCID: PMC10866073 DOI: 10.1111/1758-2229.13211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.
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Affiliation(s)
- Astrid C. H. Jaeger
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Martin Hartmann
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Rafaela Feola Conz
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Johan Six
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Emily F. Solly
- Sustainable Agroecosystems Group, Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
- Helmholtz Centre for Environmental Research—UFZLeipzigGermany
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20
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Villanova PH, Torres CMME, Jacovine LAG, Schettini BLS, Ribeiro SC, da Rocha SJSS, Rufino MPMX, de Freitas MF, Kerkoff LA. Impacts of a severe storm on carbon accumulation in coarse woody debris within a secondary Atlantic Forest fragment in Brazil. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:203. [PMID: 38277071 DOI: 10.1007/s10661-024-12316-8] [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: 09/27/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024]
Abstract
The alarming increase in extreme weather events, such as severe storms with torrential rain and strong winds, is a direct result of climate change. These events have led to discernible shifts in forest structure and the carbon cycle, primarily driven by a surge in tree mortality. However, the impacts caused by these severe storms on the production and carbon increment from coarse woody debris (CWD) are still poorly understood, especially in the Brazilian Atlantic Forest. Thus, the goal proposed by the study was to quantify the CWD volume, necromass, and carbon stock before and after the occurrence of a severe storm and to determine the importance of spatial, structural, and qualitative variables of trees in the CWD carbon increment. The increase in carbon by the storm was 2.01 MgC ha-1, with a higher concentration in the CWD less decomposed and smaller diameter class. The forest fragment plots showed distinct increments (0.05-0.35 MgC), being influenced by spatial (elevation, declivity, and slope angle) structural (basal area) and qualitative factors (trunk quality and tree health), intrinsic to the forest. Thus, it is concluded that severe storms cause a large increase in carbon in CWD, making it essential to understand the susceptibility of forests to the action of intense rains and strong winds to model and monitor the future impacts of these extreme weather events on Atlantic Forest and other tropical forests in the world.
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Affiliation(s)
- Paulo Henrique Villanova
- Departamento de Engenharia Florestal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| | | | | | | | - Sabina Cerruto Ribeiro
- Centro de Ciências Biológicas e da Natureza, Universidade Federal do Acre, Rio Branco, Acre, Brazil
| | | | | | | | - Lucas Abreu Kerkoff
- Departamento de Engenharia Florestal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Huo C, Mao J, Zhang J, Yang X, Gao S, Li J, He Q, Tang G, Xie X, Chen Z. Fertilization- and Irrigation-Modified Bacterial Community Composition and Stimulated Enzyme Activity of Eucalyptus Plantations Soil. Int J Mol Sci 2024; 25:1385. [PMID: 38338664 PMCID: PMC10855151 DOI: 10.3390/ijms25031385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/17/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
Irrigation and fertilization are essential management practices for increasing forest productivity. They also impact the soil ecosystem and the microbial population. In order to examine the soil bacterial community composition and structure in response to irrigation and fertilization in a Eucalyptus plantations, a total of 20 soil samples collected from Eucalyptus plantations were analyzed using high-throughput sequencing. Experimental treatments consisting of control (CK, no irrigation or fertilization), fertilization only (F), irrigation only (W), and irrigation and fertilization (WF). The results showed a positive correlation between soil enzyme activities (urease, cellulase, and chitinase) and fertilization treatments. These enzyme activities were also significantly correlated with the diversity of soil bacterial communities in Eucalyptus plantations.. Bacteria diversity was considerably increased under irrigation and fertilization (W, F, and WF) treatments when compared with the CK treatment. Additionally, the soil bacterial richness was increased in the Eucalyptus plantations soil under irrigation (W and WF) treatments. The Acidobacteria (38.92-47.9%), Proteobacteria (20.50-28.30%), and Chloroflexi (13.88-15.55%) were the predominant phyla found in the Eucalyptus plantations soil. Specifically, compared to the CK treatment, the relative abundance of Proteobacteria was considerably higher under the W, F, and WF treatments, while the relative abundance of Acidobacteria was considerably lower. The contents of total phosphorus, accessible potassium, and organic carbon in the soil were all positively associated with fertilization and irrigation treatments. Under the WF treatment, the abundance of bacteria associated with nitrogen and carbon metabolisms, enzyme activity, and soil nutrient contents showed an increase, indicating the positive impact of irrigation and fertilization on Eucalyptus plantations production. Collectively, these findings provide the scientific and managerial bases for improving the productivity of Eucalyptus plantations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zujing Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (C.H.); (J.M.); (J.Z.); (X.Y.); (S.G.); (J.L.); (Q.H.); (G.T.); (X.X.)
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22
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Wu H, Cui H, Fu C, Li R, Qi F, Liu Z, Yang G, Xiao K, Qiao M. Unveiling the crucial role of soil microorganisms in carbon cycling: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168627. [PMID: 37977383 DOI: 10.1016/j.scitotenv.2023.168627] [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: 09/25/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.
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Affiliation(s)
- Haowei Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Huiling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Chenxi Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ran Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Fengyuan Qi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhelun Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Keqing Xiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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23
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Meng Y, Geng X, Zhu P, Bai X, Zhang P, Ni G, Hou Y. Enhanced mutualism: A promotional effect driven by bacteria during the early invasion of Phytolacca americana. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2742. [PMID: 36107405 DOI: 10.1002/eap.2742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
The enhanced mutualism hypothesis postulates that invasive plants promote self-growth by enriching beneficial microbes to establish a positive soil feedback. However, the roles of soil microorganisms may vary with increasing time for plant growth. Research on changes in soil microbial communities over time has important implications for understanding the mechanisms underlying plant invasion. Due to the difficulty in evaluating the duration of plant growth, few studies have quantified the changes in soil microorganisms with increasing plant age. This study focuses on the invasive weed Phytolacca americana L., which has growth rings in the main root. We conducted a two-stage experiment in the field and greenhouse to explore the soil feedback changes with duration of plant growth. We determined the effects of P. americana at different ages on the soil microbial community and soil properties and performed a soil inoculation experiment to quantify the influence of soil microbes on seed germination and seedling performance. We found that the content of some soil nutrients, namely total nitrogen, total phosphorus, nitrate-N, and available phosphorus, significantly decreased with increasing growth age of P. americana, whereas the available potassium showed an opposite increasing trend. The P. americana growth age also significantly influenced the soil bacterial community structure. However, this phenomenon did not occur in the fungal community. In the bacterial community, the relative abundance of plant growth-promoting bacteria showed an increasing trend. The soil inoculation experiment had high seed germination rates and biomass accumulation when the plants were grown in conditioned soil from P. americana growth within 5 years, suggesting a positive plant-soil feedback. However, the promoting effect disappeared in conditioned soil from 10 years of age. Our findings demonstrate that plant growth-promoting bacteria significantly accumulated in the soil during the early stages of P. americana invasion, and that the strength of enhanced positive feedback may play a crucial role in facilitating P. americana invasion. This study highlights the changing nature of plant-microbe interactions during biological invasion and illustrates how bacteria could contribute to the initial success of P. americana, providing new insights into the underlying mechanisms of plant invasion.
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Affiliation(s)
- Yunhao Meng
- College of Life Sciences, Ludong University, Yantai, China
| | - Xinze Geng
- College of Life Sciences, Ludong University, Yantai, China
| | - Ping Zhu
- College of Life Sciences, Ludong University, Yantai, China
| | - Xinfu Bai
- College of Life Sciences, Ludong University, Yantai, China
| | - Ping Zhang
- College of Life Sciences, Ludong University, Yantai, China
| | - Guangyan Ni
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yuping Hou
- College of Life Sciences, Ludong University, Yantai, China
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24
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Zuo S, Wu D, Du Z, Xu C, Tan Y, Bol R, Wu W. Mitigation of soil N 2O emissions by decomposed straw based on changes in dissolved organic matter and denitrifying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167148. [PMID: 37730058 DOI: 10.1016/j.scitotenv.2023.167148] [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: 03/18/2023] [Revised: 08/19/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023]
Abstract
The return of decomposed straw represents a less explored potential option for reducing N2O emissions. However, the mechanisms underlying the effects of decomposed straw return on soil N2O mitigation are still not fully clear. Therefore, we used a helium atmosphere robotized continuous flow incubation system to compare the soil N2O and N2 emissions from four treatments: CK (control: no straw), WS (wheat straw), IWS (wheat straw decomposed with Irpex lacteus), and PWS (wheat straw decomposed with Phanerochaete chrysosporium). All the treatments have been fertilized with the same amount of KNO3. Furthermore, we also analyzed i) the chemodiversity of soil dissolved organic matter (DOM), ii) the nirS, nirK, and nosZ gene copies and relative abundances of denitrifying bacterial communities (DBCs), and iii) the specific linkages between N2O emissions and DOM and DBC. The results showed that the WS, IWS and PWS treatments increased N2O emissions compared to the CK treatment. However, applying decomposed straw to soil, especially straw treated with P. chrysosporium, effectively decreased the soil N2O and increased N2 emissions compared to WS and IWS. Moreover, the IWS and PWS treatments increased the CHO composition, but they decreased the CHON and CHOS compositions of heteroatomic compounds of DOM compared with the WS and CK treatments. Furthermore, the WS, IWS and PWS treatments all significantly increased the nirS and nosZ gene copies compared with the CK treatment. Additionally, compared with the other treatments, the PWS treatment significantly shaped the DBC and led to a higher relative abundance of Pseudomonas with nirS and nosZ genes. Meanwhile, Network analysis showed that the mitigation of N2O was closely related to particular DOM molecules, and specific DBC taxa. These results highlight the potential for decomposed straw amendments to mitigate of soil N2O emissions not only by changing soil DOM but also mediating the soil DBC.
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Affiliation(s)
- Sasa Zuo
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Department of Agricultural Engineering, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Di Wu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Zhangliu Du
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Chuncheng Xu
- Department of Agricultural Engineering, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Yuechen Tan
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing 100091, China
| | - Roland Bol
- Institute of Bio- and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; School of Natural Sciences, Environment Centre Wales, Bangor University, Bangor LL57 2UW, UK
| | - Wenliang Wu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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25
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Wang M, Pu W, Wang S, Zeng X, Sui X, Wang X. pH-Related Changes in Soil Bacterial Communities in the Sanjiang Plain, Northeast China. Microorganisms 2023; 11:2950. [PMID: 38138094 PMCID: PMC10745975 DOI: 10.3390/microorganisms11122950] [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: 10/25/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Soil bacteria are crucial components of terrestrial ecosystems, playing an important role in soil biogeochemical cycles. Although bacterial community diversity and composition are regulated by many abiotic and biotic factors, how soil physiochemical properties impact the soil bacteria community diversity and composition in wetland ecosystems remains largely unknown. In this study, we used high-throughput sequencing technology to investigate the diversity and composition of a soil bacterial community, as well as used the structural equation modeling (SEM) method to investigate the relationships of the soil's physicochemical properties (i.e., soil pH, soil organic carbon (SOC), total nitrogen (TN), ammonium nitrogen (NH4+N), electrical conductivity (EC) and nitrate nitrogen (NO3-N)), and soil bacterial community structures in three typical wetland sites in the Sanjiang Plain wetland. Our results showed that the soil physicochemical properties significantly changed the α and β-diversity of the soil bacteria communities, e.g., soil TN, NH4+N, NO3-N, and SOC were the main soil factors affecting the soil bacterial α-diversity. The soil TN and pH were the key soil factors affecting the soil bacterial community. Our results suggest that changes in soil pH indirectly affect soil bacterial communities by altering the soil nitrogenous nutrient content.
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Affiliation(s)
- 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; (M.W.); (W.P.); (S.W.)
| | - Wenmiao Pu
- 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; (M.W.); (W.P.); (S.W.)
| | - Shenzheng 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; (M.W.); (W.P.); (S.W.)
| | - Xiannan Zeng
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences, Harbin 150088, 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; (M.W.); (W.P.); (S.W.)
| | - Xin 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; (M.W.); (W.P.); (S.W.)
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26
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Yu J, Li S, Sun X, Zhou W, He L, Zhao G, Chen Z, Bai X, Zhang J. The Impact and Determinants of Mountainous Topographical Factors on Soil Microbial Community Characteristics. Microorganisms 2023; 11:2878. [PMID: 38138022 PMCID: PMC10746091 DOI: 10.3390/microorganisms11122878] [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: 10/23/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Soil bacterial and fungal community communities play significant ecological functions in mountain ecosystems. However, it is not clear how topographic factors and soil physicochemical properties influence changes in microbial community structure and diversity. This study aims to investigate how altitude and slope orientation affect soil physicochemical properties, soil microbial communities, and their contributing factors. The assessment was conducted using Illumina MiSeq sequencing in various altitude gradients and on slopes with different aspects (shady slopes and sunny slopes) in the subalpine meadow of Dongling Mountain, Beijing. Topographical factors had a significant effect on soil physicochemical properties: the primary factors determining the structure of microbial communities are total potassium (TK), ammonium nitrogen (NH4+-N), and soil organic carbon (SOC). There was no significant change in the diversity of the bacterial community, whereas the diversity of the fungal community displayed a single-peaked trend. The effect of slope orientation on microbial communities was not as significant as the effect of elevation on them. The number of bacterial communities with significant differences showed a unimodal trend, while the number of fungal communities showed a decreasing trend. The co-occurrence network of fungal communities exhibits greater intricacy than that of bacterial communities, and bacterial communities are more complex in soils with sunny slopes compared to soils with shady slopes, and the opposite is true for fungal communities. The identification of the main factors that control soil microbial diversity and composition in this study, provided the groundwork for investigating the soil microbial response and adaptation to environmental changes in subalpine meadows.
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Affiliation(s)
- Jiantao Yu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Suyan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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27
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Tao S, Veen GFC, Zhang N, Yu T, Qu L. Tree and shrub richness modifies subtropical tree productivity by regulating the diversity and community composition of soil bacteria and archaea. MICROBIOME 2023; 11:261. [PMID: 37996939 PMCID: PMC10666335 DOI: 10.1186/s40168-023-01676-x] [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: 07/24/2022] [Accepted: 09/26/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Declines in plant biodiversity often have negative consequences for plant community productivity, and it becomes increasingly acknowledged that this may be driven by shifts in soil microbial communities. So far, the role of fungal communities in driving tree diversity-productivity relationships has been well assessed in forests. However, the role of bacteria and archaea, which are also highly abundant in forest soils and perform pivotal ecosystem functions, has been less investigated in this context. Here, we investigated how tree and shrub richness affects stand-level tree productivity by regulating bacterial and archaeal community diversity and composition. We used a landscape-scale, subtropical tree biodiversity experiment (BEF-China) where tree (1, 2, or 4 species) and shrub richness (0, 2, 4, 8 species) were modified. RESULTS Our findings indicated a noteworthy decline in soil bacterial α-diversity as tree species richness increased from monoculture to 2- and 4- tree species mixtures, but a significant increase in archaeal α-diversity. Additionally, we observed that the impact of shrub species richness on microbial α-diversity was largely dependent on the level of tree species richness. The increase in tree species richness greatly reduced the variability in bacterial community composition and the complexity of co-occurrence network, but this effect was marginal for archaea. Both tree and shrub species richness increased the stand-level tree productivity by regulating the diversity and composition of bacterial community and archaeal diversity, with the effects being mediated via increases in soil C:N ratios. CONCLUSIONS Our findings provide insight into the importance of bacterial and archaeal communities in driving the relationship between plant diversity and productivity in subtropical forests and highlight the necessity for a better understanding of prokaryotic communities in forest soils. Video Abstract.
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Affiliation(s)
- Siqi Tao
- State Key Laboratory of Effecient Production of Forest Resources, Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, People's Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, 518000, Shuangyashan, People's Republic of China
| | - G F Ciska Veen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Droevendaalstesteeg 10, Wageningen, 6708 PB, the Netherlands
| | - Naili Zhang
- State Key Laboratory of Effecient Production of Forest Resources, Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, People's Republic of China.
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, 518000, Shuangyashan, People's Republic of China.
| | - Tianhe Yu
- Department of Biology, Mudanjiang Normal University, Mudanjiang, 157011, People's Republic of China
| | - Laiye Qu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing, 100085, People's Republic of China.
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28
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Luo H, Wang C, Zhang K, Ming L, Chu H, Wang H. Elevational changes in soil properties shaping fungal community assemblages in terrestrial forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165840. [PMID: 37516167 DOI: 10.1016/j.scitotenv.2023.165840] [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: 12/11/2022] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 07/31/2023]
Abstract
Environmental variables shifted by climate change act as driving factors in determining plant-associated microbial communities in terrestrial ecosystems. However, how elevation-induced changes in soil properties shape the microbial community in forest ecosystems remains less understood. Thus, the Pinus tabuliformis forests at elevations of 1500 m, 1900 m, and 2300 m above sea level were investigated to explore the effect of environmental factors on microbial assemblage. Significant changes in the soil physicochemical properties were found across the investigated elevations, such as soil moisture, temperature, pH, nitrogen (N), and phosphorus (P). Soil enzymatic activities, including soil sucrase, phosphatase, and dehydrogenase, were significantly affected by elevation, and sucrase showed a linear correlation with soil organic matter. Furthermore, the richness of fungal communities in the rhizosphere was decreased as elevation increased, while a humpback pattern was found for roots. Certain core microbiota members, such as Agaricomycetes, Leotiomycetes, and Pezizomycetes, were crucial in maintaining a stable ecological niche in both the root and rhizosphere. We also found that shifting of fungal communities in the rhizosphere were more related to physical properties (e.g., pH, soil moisture, and soil temperature), while changes in root fungal communities along elevation gradient were related mostly to soil nutrients (e.g., soil N and P). Overall, this study demonstrates that the assemblage of the root and rhizosphere fungal communities in P. tabuliformis forest primarily depends on elevation-induced changes in environmental variables and highlights the importance of predicting fungal responses to future climate change.
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Affiliation(s)
- Huan Luo
- College of Forestry, Northwest A&F University, Yangling, China; Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Chunyan Wang
- College of Forestry, Northwest A&F University, Yangling, China
| | - Kaile Zhang
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL, USA
| | - Li Ming
- College of Forestry, Northwest A&F University, Yangling, China; China University of Mining and Technology, School of Mechanics and Civil Engineering, China
| | - Honglong Chu
- College of Forestry, Northwest A&F University, Yangling, China; College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, China
| | - Haihua Wang
- College of Forestry, Northwest A&F University, Yangling, China; North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL, USA.
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29
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Pang W, Zhang P, Zhang Y, Zhang X, Huang Y, Zhang T, Liu B. The Ectomycorrhizal Fungi and Soil Bacterial Communities of the Five Typical Tree Species in the Junzifeng National Nature Reserve, Southeast China. PLANTS (BASEL, SWITZERLAND) 2023; 12:3853. [PMID: 38005750 PMCID: PMC10675191 DOI: 10.3390/plants12223853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023]
Abstract
To explore the contribution of microorganisms to forest ecosystem function, we studied the ectomycorrhizal (ECM) fungal and soil bacterial community of the five typical tree species (Pinus massoniana, PM; Castanopsis carlesii, CC; Castanopsis eyrei, CE; Castanopsis fargesii, CF; and Keteleeria cyclolepis, KC) at the Junzifeng National Nature Reserve. The results indicated that the ECM fungal and soil bacterial diversity of CC and CF was similar, and the diversity rates of CC and CF were higher than those of PM, CE, and KC. Cenococcum geophilum and unclassified_Cortinariaceae II were the most prevalent occurring ECM fungi species in the five typical tree species, followed by unclassified_Cortinariaceae I and Lactarius atrofuscus. In bacteria, the dominant bacterial genera were Acidothermus, Bradyrhizobium, Acidibacter, Candidatus_Solibacter, Candidatus_Koribacter, Roseiarcus, and Bryobacter. EMF fungi and soil bacteria were correlated with edaphic factors, especially the soil pH, TP, and TK, caused by stand development. The results show that the community characteristics of ECM fungi and bacteria in the typical tree species of the Junzifeng National Nature Reserve reflect the critical role of soil microorganisms in stabilizing forest ecosystems.
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Affiliation(s)
- Wenbo Pang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Panpan Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Yuhu Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Xiao Zhang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yanbin Huang
- Administration Bureau of Fujian Junzifeng National Nature Reserve, Mingxi 365200, China;
| | - Taoxiang Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Bao Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
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30
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Błońska E, Lasota J, Kempf M, Ostonen I. The nutritional status and root development of silver fir (Abies alba Mill.) seedlings growing on decaying deadwood in temperate forest ecosystem. Sci Rep 2023; 13:17813. [PMID: 37857689 PMCID: PMC10587165 DOI: 10.1038/s41598-023-45187-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023] Open
Abstract
The study aimed to compare two substrates, soil and deadwood, for the regeneration of silver fir (Abies alba Mill.) seedlings. Three-year-old fir seedlings growing both on deadwood and in the soil were collected. The examination involved determining the physical, chemical, and biochemical properties of soil and deadwood, as well as assessing the morphology of the roots and the nutrition of seedlings growing on the soil and deadwood. The examined substrates differed in physical, chemical and biochemical properties. It was shown that strongly decomposed fir logs are a good substrate for the growth of fir seedlings, mainly due to the high content of exchangeable cations (especially calcium, magnesium and potassium) and high phosphorus and nitrogen content. The type of substrate had a significant impact on the root morphology of fir seedlings. In our study, the most responsive root traits to differences in growing substrates were specific root area (SRA) and specific root length (SRL). Our analyses did not confirm significant differences in the stoichiometry of C, N and P in the roots and needles of seedlings grown on different substrates. The stoichiometry of roots and needles suggests no limitations in the uptake of nutrients by seedlings growing on deadwood. This study validated that heavily decomposed wood can provide favourable microhabitats for the growth of the young generation of fir.
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Affiliation(s)
- Ewa Błońska
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture, Al. 29 Listopada 46, 31-425, Kraków, Poland
| | - Jarosław Lasota
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture, Al. 29 Listopada 46, 31-425, Kraków, Poland
| | - Marta Kempf
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture, Al. 29 Listopada 46, 31-425, Kraków, Poland.
| | - Ivika Ostonen
- Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
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Cheng G, Zhang X, Zhu M, Zhang Z, Jing L, Wang L, Li Q, Zhang X, Wang H, Wang W. Tree diversity, growth status, and spatial distribution affected soil N availability and N 2O efflux: Interaction with soil physiochemical properties. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118375. [PMID: 37356331 DOI: 10.1016/j.jenvman.2023.118375] [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: 12/01/2022] [Revised: 06/04/2023] [Accepted: 06/10/2023] [Indexed: 06/27/2023]
Abstract
Soil nitrogen (N) is an essential nutrient for tree growth, and excessive N is a source of pollution. This paper aims to define the effects of plant diversity and forest structure on various aspects of soil N cycling. Herein, we collected soils from 720 plots to measure total N content (TN), alkali-hydrolyzed N (AN), nitrate N (NO3--N), ammonium N (NH4+-N) in a 7.2 ha experimental forest in northeast China. Four plant diversity indices, seven structural metrics, four soil properties, and in situ N2O efflux were also measured. We found that: 1) high tree diversity had 1.3-1.4-fold NO3--N, 1.1-fold NH4+-N, and 1.5-1.8-fold N2O efflux (p < 0.05). 2) Tree growth decreased soil TN, AN, and NO3--N by more than 13%, and tree mixing and un-uniform distribution increased TN, AN, and NH4+-N by 11-22%. 3) Soil organic carbon (SOC) explained 34.3% of the N variations, followed by soil water content (1.5%), tree diameter (1.5%) and pH (1%), and soil bulk density (0.5%). SOC had the most robust linear relations to TN (R2 = 0.59) and AN (R2 = 0.5). 4) The partial least squares path model revealed that the tree diversity directly increased NO3--N, NH4+-N, and N2O efflux, and they were strengthened indirectly from soil properties by 1%-4%. The effects of tree size-density (-0.24) and spatial structure (0.16) were mainly achieved via their soil interaction and thus indirectly decreased NH4+-N, AN, and TN. Overall, high tree diversity forests improved soil N availability and N2O efflux, and un-uniform spatial tree assemblages could partially balance the soil N consumed by tree growth. Our data support soil N management in high northern hemisphere temperate forests from tree diversity and forest structural regulations.
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Affiliation(s)
- Guanchao Cheng
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Xu Zhang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Meina Zhu
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Zhonghua Zhang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Lixin Jing
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Lei Wang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Qi Li
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Xiting Zhang
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Huimei Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
| | - Wenjie Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China; Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, CAS, Changchun, 130102, China.
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Zabłotni A, Kaliński A, Glądalski M, Markowski M, Skwarska J, Wawrzyniak J, Bańbura J. Nest Box Bacterial Loads Are Affected by Cavity Use by Secondary Hole Nesters. Animals (Basel) 2023; 13:2989. [PMID: 37760389 PMCID: PMC10526079 DOI: 10.3390/ani13182989] [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: 07/13/2023] [Revised: 08/18/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Among the environmental factors that affect bird nesting in nest boxes, the influence of microbial communities is relatively poorly understood. In this study, nest boxes used for breeding by secondary cavity nesters were sampled before the start of the breeding season to assess the bacterial loads of the nest box in relation to their previous year status. Different parts of the wooden nest box offer variable conditions for the development of bacteria. During the breeding season, the nest box entrance hole is wiped out by birds, delivering bacteria to their bodies, but during winter, it is exposed to unfavourable external conditions. The interior of the nest box, in turn, is also wiped by birds, but the conditions during winter are more stable there. Therefore, samples from the entrance hole and the interior of the nest box were taken at two different study sites: an urban parkland and a natural forest. We predicted that both the occupancy of the nest boxes during the previous breeding season by birds and the nesting sites would influence the bacterial load of the nest box. To verify this prediction, two categories of nest boxes were sampled at both study sites: nest boxes occupied by any of the two tit species (Great Tit or Blue Tit) in the previous season for breeding and nest boxes that had remained empty that year. The interior bacterial load of the nest box was higher in the nest boxes occupied in the previous breeding season, but only in the forest area. Furthermore, the bacterial load of both the entrance hole of the nest box and the interior was significantly higher in the forest study area in both occupied and unoccupied nest boxes. Our results show that the bacterial load of the nest box is positively related to the presence of nests in the previous breeding season and can vary between different sites.
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Affiliation(s)
- Agnieszka Zabłotni
- Laboratory of General Microbiology, Department of Biology of Bacteria, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland;
| | - Adam Kaliński
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; (M.G.); (M.M.); (J.S.); (J.W.); (J.B.)
| | - Michał Glądalski
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; (M.G.); (M.M.); (J.S.); (J.W.); (J.B.)
| | - Marcin Markowski
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; (M.G.); (M.M.); (J.S.); (J.W.); (J.B.)
| | - Joanna Skwarska
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; (M.G.); (M.M.); (J.S.); (J.W.); (J.B.)
| | - Jarosław Wawrzyniak
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; (M.G.); (M.M.); (J.S.); (J.W.); (J.B.)
| | - Jerzy Bańbura
- Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland; (M.G.); (M.M.); (J.S.); (J.W.); (J.B.)
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Zhu GX, Chen X, Wu YJ, Wang HL, Jiao Y, Liu ZC, Zhang Y, Tang SK, Kong DJ, Cao YR. Chryseobacterium luquanense sp. nov., a casein-hydrolysing bacterium from the Jiaozi Mountain in Yunnan, PR China. Int J Syst Evol Microbiol 2023; 73. [PMID: 37728599 DOI: 10.1099/ijsem.0.006031] [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] [Indexed: 09/21/2023] Open
Abstract
Strain KC 927T was isolated during an investigation of the soil bacteria diversity on Jiaozi Mountain, central Yunnan, Southwest China. The strain was Gram-stain-negative, rod-shaped, non-motile, oxidase-negative, catalase-positive and aerobic. Results of 16S rRNA gene alignment and phylogenetic analysis indicated that strain KC 927T was a member of the genus Chryseobacterium and closely related to Chryseobacterium caseinilyticum GCR10T (98.4%), Chryseobacterium piscicola DSM 21068T (98.3 %) and 'Chryseobacterium formosus' CCTCC AB 2015118T (97.9 %). With a genome size of 4 348 708 bp, strain KC 927T had 33.5 mol% DNA G+C content and contained 4012 protein-coding genes and 77 RNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain KC 927T and C. caseinilyticum GCR10T, C. piscicola DSM 21068T and 'C. formosus' CCTCC AB 2015118T were 80.1, 79.6 and 90.7 %, and 25.5, 23.6 and 42.0 %, respectively. The main polar lipid of strain KC 927T was phosphatidylethanolamine and the respiratory quinone was MK-6. The major fatty acids (≥10 %) were iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. Evidence from phenotypic, phylogenetic and chemotaxonomic analyses support that strain KC 927T represents a new species of the genus Chryseobacterium, for which the name Chryseobacterium luquanense sp. nov. is proposed. The type strain is KC 927T (=CGMCC 1.18760T=JCM 35707T).
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Affiliation(s)
- Guo-Xing Zhu
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Xiu Chen
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
- School of Medicine, Kunming University, Kunming, Yunnan, PR China
| | - Ya-Jie Wu
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Hai-Long Wang
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Yu Jiao
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Zi-Chao Liu
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Yue Zhang
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, PR China
| | - De-Jun Kong
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, PR China
| | - Yan-Ru Cao
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, PR China
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Fuller E, Germaine KJ, Rathore DS. The Good, the Bad, and the Useable Microbes within the Common Alder ( Alnus glutinosa) Microbiome-Potential Bio-Agents to Combat Alder Dieback. Microorganisms 2023; 11:2187. [PMID: 37764031 PMCID: PMC10535473 DOI: 10.3390/microorganisms11092187] [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: 07/17/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Common Alder (Alnus glutinosa (L.) Gaertn.) is a tree species native to Ireland and Europe with high economic and ecological importance. The presence of Alder has many benefits including the ability to adapt to multiple climate types, as well as aiding in ecosystem restoration due to its colonization capabilities within disturbed soils. However, Alder is susceptible to infection of the root rot pathogen Phytophthora alni, amongst other pathogens associated with this tree species. P. alni has become an issue within the forestry sector as it continues to spread across Europe, infecting Alder plantations, thus affecting their growth and survival and altering ecosystem dynamics. Beneficial microbiota and biocontrol agents play a crucial role in maintaining the health and resilience of plants. Studies have shown that beneficial microbes promote plant growth as well as aid in the protection against pathogens and abiotic stress. Understanding the interactions between A. glutinosa and its microbiota, both beneficial and pathogenic, is essential for developing integrated management strategies to mitigate the impact of P. alni and maintain the health of Alder trees. This review is focused on collating the relevant literature associated with Alder, current threats to the species, what is known about its microbial composition, and Common Alder-microbe interactions that have been observed worldwide to date. It also summarizes the beneficial fungi, bacteria, and biocontrol agents, underpinning genetic mechanisms and secondary metabolites identified within the forestry sector in relation to the Alder tree species. In addition, biocontrol mechanisms and microbiome-assisted breeding as well as gaps within research that require further attention are discussed.
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Affiliation(s)
- Emma Fuller
- EnviroCore, Dargan Research Centre, Department of Applied Science, South East Technological University, Kilkenny Road, R93 V960 Carlow, Ireland; (E.F.); (K.J.G.)
- Teagasc, Forestry Development Department, Oak Park Research Centre, R93 XE12 Carlow, Ireland
| | - Kieran J. Germaine
- EnviroCore, Dargan Research Centre, Department of Applied Science, South East Technological University, Kilkenny Road, R93 V960 Carlow, Ireland; (E.F.); (K.J.G.)
| | - Dheeraj Singh Rathore
- Teagasc, Forestry Development Department, Oak Park Research Centre, R93 XE12 Carlow, Ireland
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Zhang J, Liu Q, Wang D, Zhang Z. Soil Microbial Community, Soil Quality, and Productivity along a Chronosequence of Larix principis-rupprechtii Forests. PLANTS (BASEL, SWITZERLAND) 2023; 12:2913. [PMID: 37631125 PMCID: PMC10458017 DOI: 10.3390/plants12162913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/27/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023]
Abstract
Elucidating the correlation between soil microbial communities and forest productivity is the focus of research in the field of forest ecology. Nonetheless, the relationship between stand age, soil quality, soil microorganisms, and their combined influence on productivity is still unclear. In this study, five development stages (14, 25, 31, 39, and >80 years) of larch (Larix principis-rupprechtii) forests were investigated in Inner Mongolia and Shanxi provinces of China. We evaluated soil quality using the Integrated Soil Quality Index (SQI) and analyzed changes in bacterial and fungal communities using high-throughput sequencing. Regression models were also established to examine the impacts of stand age, microbial diversity, and SQI on productivity. The findings revealed an ascending trend in soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), available potassium (AK), and SQI in 14, 25, 31, and 39-year-old stands. The abundance of oligotrophic bacteria Acidobacteria exhibited a gradual decline with increasing forest age, whereas copiotroph bacteria Proteobacteria displayed a progressive increase. Stands older than 80 years exhibited a higher abundance of both the saprophytic fungus Ascomycota and mycorrhizal fungus Basidiomycota. Forest age had a significant impact on microbial diversity, particularly in terms of bacterial diversity, impacting both α and β diversity. The soil bacterial community structure was influenced by AK, SOM, TN, TP, and pH. Conversely, the fungal community structure was regulated by crucial factors including SOM, TN, TP, TK, AK, and pH. Fungal diversity demonstrated a significant and positive correlation with the basal area increment (BAI) of larch. Furthermore, microbial diversity accounted for 23.6% of the variation in BAI. In summary, the findings implied a robust association between microbial composition, diversity, and soil chemical properties throughout the chronosequence of larch forests. These factors collectively played a crucial role in influencing the productivity of larch forest.
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Affiliation(s)
| | | | | | - Zhidong Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071001, China; (J.Z.); (Q.L.); (D.W.)
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Mazumdar R, Saikia K, Thakur D. Potentiality of Actinomycetia Prevalent in Selected Forest Ecosystems in Assam, India to Combat Multi-Drug-Resistant Microbial Pathogens. Metabolites 2023; 13:911. [PMID: 37623855 PMCID: PMC10456813 DOI: 10.3390/metabo13080911] [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: 05/08/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Actinomycetia are known for their ability to produce a wide range of bioactive secondary metabolites having significant therapeutic importance. This study aimed to explore the potential of actinomycetia as a source of bioactive compounds with antimicrobial properties against multi-drug-resistant (MDR) clinical pathogens. A total of 65 actinomycetia were isolated from two unexplored forest ecosystems, namely the Pobitora Wildlife Sanctuary (PWS) and the Deepor Beel Wildlife Sanctuary (DBWS), located in the Indo-Burma mega-biodiversity hotspots of northeast India, out of which 19 isolates exhibited significant antimicrobial activity. 16S rRNA gene sequencing was used for the identification and phylogenetic analysis of the 19 potent actinomycetia isolates. The results reveal that the most dominant genus among the isolates was Streptomyces (84.21%), followed by rare actinomycetia genera such as Nocardia, Actinomadura, and Nonomuraea. Furthermore, seventeen of the isolates tested positive for at least one antibiotic biosynthetic gene, specifically type II polyketide synthase (PKS-II) and nonribosomal peptide synthetases (NRPSs). These genes are associated with the production of bioactive compounds with antimicrobial properties. Among the isolated strains, three actinomycetia strains, namely Streptomyces sp. PBR1, Streptomyces sp. PBR36, and Streptomyces sp. DBR11, demonstrated the most potent antimicrobial activity against seven test pathogens. This was determined through in vitro antimicrobial bioassays and the minimum inhibitory concentration (MIC) values of ethyl acetate extracts. Gas chromatography-mass spectrometry (GS-MS) and whole-genome sequencing (WGS) of the three strains revealed a diverse group of bioactive compounds and secondary metabolite biosynthetic gene clusters (smBGCs), respectively, indicating their high therapeutic potential. These findings highlight the potential of these microorganisms to serve as a valuable resource for the discovery and development of novel antibiotics and other therapeutics with high therapeutic potential.
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Affiliation(s)
- Rajkumari Mazumdar
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati 781035, India;
- Department of Molecular Biology & Biotechnology, Cotton University, Guwahati 781001, India
| | - Kangkon Saikia
- Bioinformatics Infrastructure Facility, Institute of Advanced Study in Science and Technology, Guwahati 781035, India;
| | - Debajit Thakur
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology (IASST), Guwahati 781035, India;
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Yang J, Lu J, Yang Y, Tian K, Kong X, Tian X, Scheu S. Earthworms neutralize the influence of components of particulate pollutants on soil extracellular enzymatic functions in subtropical forests. PeerJ 2023; 11:e15720. [PMID: 37551350 PMCID: PMC10404396 DOI: 10.7717/peerj.15720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/16/2023] [Indexed: 08/09/2023] Open
Abstract
Human activities are increasing the input of atmospheric particulate pollutants to forests. The components of particulate pollutants include inorganic anions, base cations and hydrocarbons. Continuous input of particulate pollutants may affect soil functioning in forests, but their effects may be modified by soil fauna. However, studies investigating how soil fauna affects the effects of particulate pollutants on soil functioning are lacking. Here, we investigated how earthworms and the particulate components interact in affecting soil enzymatic functions in a deciduous (Quercus variabilis) and a coniferous (Pinus massoniana) forest in southeast China. We manipulated the addition of nitrogen (N, ammonium nitrate), sodium (Na, sodium chloride) and polycyclic aromatic hydrocarbons (PAHs, five mixed PAHs) in field mesocosms with and without Eisenia fetida, an earthworm species colonizing forests in eastern China. After one year, N and Na addition increased, whereas PAHs decreased soil enzymatic functions, based on average Z scores of extracellular enzyme activities. Earthworms generally stabilized soil enzymatic functions via neutralizing the effects of N, Na and PAHs addition in the deciduous but not in the coniferous forest. Specifically, earthworms neutralized the effects of N and Na addition on soil pH and the effects of the addition of PAHs on soil microbial biomass. Further, both particulate components and earthworms changed the correlations among soil enzymatic and other ecosystem functions in the deciduous forest, but the effects depended on the type of particulate components. Generally, the effects of particulate components and earthworms on soil enzymatic functions were weaker in the coniferous than the deciduous forest. Overall, the results indicate that earthworms stabilize soil enzymatic functions in the deciduous but not the coniferous forest irrespective of the type of particulate components. This suggests that earthworms may neutralize the influence of atmospheric particulate pollutants on ecosystem functions, but the neutralization may be restricted to deciduous forests.
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Affiliation(s)
- Junbo Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Lower Saxony, Germany
| | - Jingzhong Lu
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Lower Saxony, Germany
| | - Yinghui Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China
| | - Kai Tian
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, Henan Province, China
| | - Xiangshi Kong
- Key Laboratory for Ecotourism of Hunan Province, School of Tourism and Management Engineering, Jishou University, Jishou, Hunan Province, China
| | - Xingjun Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai Province, China
| | - Stefan Scheu
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Lower Saxony, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Lower Saxony, Germany
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Gonzalez JM, Santana MM, Gomez EJ, Delgado JA. Soil Thermophiles and Their Extracellular Enzymes: A Set of Capabilities Able to Provide Significant Services and Risks. Microorganisms 2023; 11:1650. [PMID: 37512823 PMCID: PMC10386326 DOI: 10.3390/microorganisms11071650] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
During this century, a number of reports have described the potential roles of thermophiles in the upper soil layers during high-temperature periods. This study evaluates the capabilities of these microorganisms and proposes some potential consequences and risks associated with the activity of soil thermophiles. They are active in organic matter mineralization, releasing inorganic nutrients (C, S, N, P) that otherwise remain trapped in the organic complexity of soil. To process complex organic compounds in soils, these thermophiles require extracellular enzymes to break down large polymers into simple compounds, which can be incorporated into the cells and processed. Soil thermophiles are able to adapt their extracellular enzyme activities to environmental conditions. These enzymes can present optimum activity under high temperatures and reduced water content. Consequently, these microorganisms have been shown to actively process and decompose substances (including pollutants) under extreme conditions (i.e., desiccation and heat) in soils. While nutrient cycling is a highly beneficial process to maintain soil service quality, progressive warming can lead to excessive activity of soil thermophiles and their extracellular enzymes. If this activity is too high, it may lead to reduction in soil organic matter, nutrient impoverishment and to an increased risk of aridity. This is a clear example of a potential effect of future predicted climate warming directly caused by soil microorganisms with major consequences for our understanding of ecosystem functioning, soil health and the risk of soil aridity.
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Affiliation(s)
- Juan M Gonzalez
- Institute of Natural Resources and Agrobiology, IRNAS-CSIC, Avda. Reina Mercedes 10, E-41012 Sevilla, Spain
| | - Margarida M Santana
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Enrique J Gomez
- Institute of Natural Resources and Agrobiology, IRNAS-CSIC, Avda. Reina Mercedes 10, E-41012 Sevilla, Spain
| | - José A Delgado
- Department of Engineering, University of Loyola, Avda. de las Universidades, E-41704 Dos Hermanas, Spain
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Gonzalez JM, Aranda B. Microbial Growth under Limiting Conditions-Future Perspectives. Microorganisms 2023; 11:1641. [PMID: 37512814 PMCID: PMC10383181 DOI: 10.3390/microorganisms11071641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/02/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Microorganisms rule the functioning of our planet and each one of the individual macroscopic living creature. Nevertheless, microbial activity and growth status have always been challenging tasks to determine both in situ and in vivo. Microbial activity is generally related to growth, and the growth rate is a result of the availability of nutrients under adequate or adverse conditions faced by microbial cells in a changing environment. Most studies on microorganisms have been carried out under optimum or near-optimum growth conditions, but scarce information is available about microorganisms at slow-growing states (i.e., near-zero growth and maintenance metabolism). This study aims to better understand microorganisms under growth-limiting conditions. This is expected to provide new perspectives on the functions and relevance of the microbial world. This is because (i) microorganisms in nature frequently face conditions of severe growth limitation, (ii) microorganisms activate singular pathways (mostly genes remaining to be functionally annotated), resulting in a broad range of secondary metabolites, and (iii) the response of microorganisms to slow-growth conditions remains to be understood, including persistence strategies, gene expression, and cell differentiation both within clonal populations and due to the complexity of the environment.
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Affiliation(s)
- Juan M Gonzalez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, E-41012 Sevilla, Spain
| | - Beatriz Aranda
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, IRNAS-CSIC, E-41012 Sevilla, Spain
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Berrios L, Yeam J, Holm L, Robinson W, Pellitier PT, Chin ML, Henkel TW, Peay KG. Positive interactions between mycorrhizal fungi and bacteria are widespread and benefit plant growth. Curr Biol 2023:S0960-9822(23)00760-1. [PMID: 37369208 DOI: 10.1016/j.cub.2023.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/05/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Bacteria, ectomycorrhizal (EcM) fungi, and land plants have been coevolving for nearly 200 million years, and their interactions presumably contribute to the function of terrestrial ecosystems. The direction, stability, and strength of bacteria-EcM fungi interactions across landscapes and across a single plant host, however, remains unclear. Moreover, the genetic mechanisms that govern them have not been addressed. To these ends, we collected soil samples from Bishop pine forests across a climate-latitude gradient spanning coastal California, fractionated the soil samples based on their proximity to EcM-colonized roots, characterized the microbial communities using amplicon sequencing, and generated linear regression models showing the impact that select bacterial taxa have on EcM fungal abundance. In addition, we paired greenhouse experiments with transcriptomic analyses to determine the directionality of these relationships and identify which genes EcM-synergist bacteria express during tripartite symbioses. Our data reveal that ectomycorrhizas (i.e., EcM-colonized roots) enrich conserved bacterial taxa across climatically heterogeneous regions. We also show that phylogenetically diverse EcM synergists are positively associated with plant and fungal growth and have unique gene expression profiles compared with EcM-antagonist bacteria. In sum, we identify common mechanisms that facilitate widespread and diverse multipartite symbioses, which inform our understanding of how plants develop in complex environments.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Jay Yeam
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Wallis Robinson
- Forestry and Forest Health Program, University of California Cooperative Extension Humboldt and Del Norte Counties, Eureka, CA 95503, USA
| | | | - Mei Lin Chin
- Department of Biological Sciences, California State Polytechnic University, Humboldt, Arcata, CA 95521, USA
| | - Terry W Henkel
- Department of Biological Sciences, California State Polytechnic University, Humboldt, Arcata, CA 95521, USA
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
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Hagh-Doust N, Mikryukov V, Anslan S, Bahram M, Puusepp R, Dulya O, Tedersoo L. Effects of nitrogen deposition on carbon and nutrient cycling along a natural soil acidity gradient as revealed by metagenomics. THE NEW PHYTOLOGIST 2023; 238:2607-2620. [PMID: 36949609 DOI: 10.1111/nph.18897] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/15/2023] [Indexed: 05/19/2023]
Abstract
Nitrogen (N) deposition and soil acidification are environmental challenges affecting ecosystem functioning, health, and biodiversity, but their effects on functional genes are poorly understood. Here, we utilized metabarcoding and metagenomics to investigate the responses of soil functional genes to N deposition along a natural soil pH gradient. Soil N content was uncorrelated with pH, enabling us to investigate their effects separately. Soil acidity strongly and negatively affected the relative abundances of most cluster of orthologous gene categories of the metabolism supercategory. Similarly, soil acidity negatively affected the diversity of functional genes related to carbon and N but not phosphorus cycling. Multivariate analyses showed that soil pH was the most important factor affecting microbial and functional gene composition, while the effects of N deposition were less important. Relative abundance of KEGG functional modules related to different parts of the studied cycles showed variable responses to soil acidity and N deposition. Furthermore, our results suggested that the diversity-function relationship reported for other organisms also applies to soil microbiomes. Since N deposition and soil pH affected microbial taxonomic and functional composition to a different extent, we conclude that N deposition effects might be primarily mediated through soil acidification in forest ecosystems.
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Affiliation(s)
- Niloufar Hagh-Doust
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
- Mycology and Microbiology Center, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
| | - Vladimir Mikryukov
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
- Mycology and Microbiology Center, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
- Mycology and Microbiology Center, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 75651, Uppsala, Sweden
| | - Rasmus Puusepp
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
| | - Olesya Dulya
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
- Mycology and Microbiology Center, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Juhan Liivi 2, 50409, Tartu, Estonia
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Wang Z, Xu M, Li F, Bai Y, Hou J, Li X, Cao R, Deng Y, Jiang Y, Wang H, Yang W. Changes in soil bacterial communities and functional groups beneath coarse woody debris across a subalpine forest successional series. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
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Martín-Pinto P, Dejene T, Benucci GMN, Mediavilla O, Hernández-Rodríguez M, Geml J, Baldrian P, Sanz-Benito I, Olaizola J, Bonito G, Oria-de-Rueda JA. Co-responses of bacterial and fungal communities to fire management treatments in Mediterranean pyrophytic ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162676. [PMID: 36894081 DOI: 10.1016/j.scitotenv.2023.162676] [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: 11/25/2022] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Cistus scrublands are pyrophytic ecosystems and occur widely across Mediterranean regions. Management of these scrublands is critical to prevent major disturbances, such as recurring wildfires. This is because management appears to compromise the synergies necessary for forest health and the provision of ecosystem services. Furthermore, it supports high microbial diversity, opening questions of how forest management practices impact belowground associated diversity as research related to this issue is scarce. This study aims to investigate the effects of different fire prevention treatments and site history on bacterial and fungi co-response and co-occurrence patterns over a fire-risky scrubland ecosystem. Two different site histories were studied by applying three different fire prevention treatments and samples were analyzed by amplification and sequencing of ITS2 and 16S rDNA for fungi and bacteria, respectively. The data revealed that site history, especially regarding fire occurrence, strongly influenced the microbial community. Young burnt areas tended to have a more homogeneous and lower microbial diversity, suggesting environmental filtering to a heat-resistant community. In comparison, young clearing history also showed a significant impact on the fungal community but not on the bacteria. Some bacteria genera were efficient predictors of fungal diversity and richness. For instance, Ktedonobacter and Desertibacter were a predictor of the presence of the edible mycorrhizal bolete Boletus edulis. These results demonstrate fungal and bacterial community co-response to fire prevention treatments and provide new tools for forecasting forest management impacts on microbial communities.
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Affiliation(s)
- Pablo Martín-Pinto
- Sustainable Forest Management Research Institute, University of Valladolid, Avda. Madrid 44, 34071 Palencia, Spain.
| | - Tatek Dejene
- Sustainable Forest Management Research Institute, University of Valladolid, Avda. Madrid 44, 34071 Palencia, Spain; Ethiopian Environment and Forest Research Institute (EEFRI), P. O. Box 30708 Code 1000, Addis Ababa, Ethiopia
| | - Gian Maria Niccolò Benucci
- Michigan State University, Department of Plant, Soil and Microbial Sciences, East Lansing, MI 48824, United States of America.
| | - Olaya Mediavilla
- Sustainable Forest Management Research Institute, University of Valladolid, Avda. Madrid 44, 34071 Palencia, Spain; IDForest - Biotecnología Forestal Aplicada, Calle Curtidores, 17, 34004 Palencia, Spain.
| | - María Hernández-Rodríguez
- Sustainable Forest Management Research Institute, University of Valladolid, Avda. Madrid 44, 34071 Palencia, Spain; IDForest - Biotecnología Forestal Aplicada, Calle Curtidores, 17, 34004 Palencia, Spain.
| | - József Geml
- MTA-EKE Lendület Environmental Microbiome Research Group, Eszterházy Károly University, Leányka u. 6, 3300 Eger, Hungary.
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14200 Praha 4, Czech Republic.
| | - Ignacio Sanz-Benito
- Sustainable Forest Management Research Institute, University of Valladolid, Avda. Madrid 44, 34071 Palencia, Spain.
| | - Jaime Olaizola
- IDForest - Biotecnología Forestal Aplicada, Calle Curtidores, 17, 34004 Palencia, Spain.
| | - Gregory Bonito
- Michigan State University, Department of Plant, Soil and Microbial Sciences, East Lansing, MI 48824, United States of America.
| | - Juan Andrés Oria-de-Rueda
- Sustainable Forest Management Research Institute, University of Valladolid, Avda. Madrid 44, 34071 Palencia, Spain.
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Onyango LA, Ngonga FA, Karanja EN, Kuja JO, Boga HI, Cowan DA, Mwangi KW, Maghenda MW, Marinho Lebre PBN, Kambura AK. The soil microbiomes of forest ecosystems in Kenya: their diversity and environmental drivers. Sci Rep 2023; 13:7156. [PMID: 37130890 PMCID: PMC10154314 DOI: 10.1038/s41598-023-33993-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/21/2023] [Indexed: 05/04/2023] Open
Abstract
Soil microbiomes in forest ecosystems act as both nutrient sources and sinks through a range of processes including organic matter decomposition, nutrient cycling, and humic compound incorporation into the soil. Most forest soil microbial diversity studies have been performed in the northern hemisphere, and very little has been done in forests within African continent. This study examined the composition, diversity and distribution of prokaryotes in Kenyan forests top soils using amplicon sequencing of V4-V5 hypervariable region of the 16S rRNA gene. Additionally, soil physicochemical characteristics were measured to identify abiotic drivers of prokaryotic distribution. Different forest soils were found to have statistically distinct microbiome compositions, with Proteobacteria and Crenarchaeota taxa being the most differentially abundant across regions within bacterial and archaeal phyla, respectively. Key bacterial community drivers included pH, Ca, K, Fe, and total N while archaeal diversity was shaped by Na, pH, Ca, total P and total N. To contextualize the prokaryote diversity of Kenyan forest soils on a global scale, the sample set was compared to amplicon data obtained from forest biomes across the globe; displaying them to harbor distinct microbiomes with an over-representation of uncultured taxa such as TK-10 and Ellin6067 genera.
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Affiliation(s)
- Lorine Akinyi Onyango
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya
| | - Florence Atieno Ngonga
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya
| | - Edward Nderitu Karanja
- International Centre for Insect Physiology and Ecology, P.O. Box 30772-00100, Nairobi, Kenya
| | - Josiah Ochieng' Kuja
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya
| | - Hamadi Iddi Boga
- School of Agriculture, Earth and Environmental Sciences, Taita Taveta University, P. O. Box 635-80300, Voi, Kenya
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Marianne Wughanga Maghenda
- School of Agriculture, Earth and Environmental Sciences, Taita Taveta University, P. O. Box 635-80300, Voi, Kenya
| | - Pedro Bixirao Neto Marinho Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anne Kelly Kambura
- School of Agriculture, Earth and Environmental Sciences, Taita Taveta University, P. O. Box 635-80300, Voi, Kenya.
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Mukhtar H, Wunderlich RF, Muzaffar A, Ansari A, Shipin OV, Cao TND, Lin YP. Soil microbiome feedback to climate change and options for mitigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163412. [PMID: 37059149 DOI: 10.1016/j.scitotenv.2023.163412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 03/14/2023] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Microbes are a critical component of soil ecosystems, performing crucial functions in biogeochemical cycling, carbon sequestration, and plant health. However, it remains uncertain how their community structure, functioning, and resultant nutrient cycling, including net GHG fluxes, would respond to climate change at different scales. Here, we review global and regional climate change effects on soil microbial community structure and functioning, as well as the climate-microbe feedback and plant-microbe interactions. We also synthesize recent studies on climate change impacts on terrestrial nutrient cycles and GHG fluxes across different climate-sensitive ecosystems. It is generally assumed that climate change factors (e.g., elevated CO2 and temperature) will have varying impacts on the microbial community structure (e.g., fungi-to-bacteria ratio) and their contribution toward nutrient turnover, with potential interactions that may either enhance or mitigate each other's effects. Such climate change responses, however, are difficult to generalize, even within an ecosystem, since they are subjected to not only a strong regional influence of current ambient environmental and edaphic conditions, historical exposure to fluctuations, and time horizon but also to methodological choices (e.g., network construction). Finally, the potential of chemical intrusions and emerging tools, such as genetically engineered plants and microbes, as mitigation strategies against global change impacts, particularly for agroecosystems, is presented. In a rapidly evolving field, this review identifies the knowledge gaps complicating assessments and predictions of microbial climate responses and hindering the development of effective mitigation strategies.
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Affiliation(s)
- Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | | | | | - Andrianto Ansari
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | - Oleg V Shipin
- School of Environmental Engineering and Management, Asian Institute of Technology, Thailand
| | - Thanh Ngoc-Dan Cao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | - Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan.
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46
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Baldrian P, López-Mondéjar R, Kohout P. Forest microbiome and global change. Nat Rev Microbiol 2023:10.1038/s41579-023-00876-4. [PMID: 36941408 DOI: 10.1038/s41579-023-00876-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/23/2023]
Abstract
Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant-microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
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Xie L, Li W, Pang X, Liu Q, Yin C. Soil properties and root traits are important factors driving rhizosphere soil bacterial and fungal community variations in alpine Rhododendron nitidulum shrub ecosystems along an altitudinal gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161048. [PMID: 36563760 DOI: 10.1016/j.scitotenv.2022.161048] [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: 09/05/2022] [Revised: 12/02/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Both soil properties and plant root traits are pivotal factors affecting microbial communities. However, there is still limited information about their importance in shaping rhizosphere soil microbial communities, particularly in less-studied alpine shrub ecosystems. To investigate the effects of altitude (3300, 3600, 3900, and 4200 m) on the diversity and composition of rhizosphere soil bacterial and fungal communities, as well as the factors shaping rhizosphere soil microbial communities, we conducted this study in alpine Rhododendron nitidulum shrub ecosystems from the Zheduo mountain of the eastern Tibetan Plateau. Results demonstrated that bacterial community diversity and richness decreased to the lowest value at 3600 m and then increased at higher altitudes compared with 3300 m; whereas fungal richness at 3300 m was much lower than at other altitudes, and was closely related to soil properties and root traits. The composition of rhizosphere soil bacterial and fungal communities at the low altitude (3300 m) was different from that at high altitudes. Permutational multivariate analysis of variance and redundancy analysis indicated that soil properties (soil water content, pH, NO3--N, and available phosphorus) and root traits (surface area, and maximum depth) were the major factors explaining the variations of rhizosphere soil bacterial and fungal communities. Specific bacterial and fungal taxa along altitudes were identified. The bacterial taxa Planctomycetota was dominant at 3300 and 3600 m with low soil nutrient availability and high root surface area, whereas the fungal taxa Mortierellomycota was abundant at 3900 and 4200 m with high soil nutrient availability and low root surface area. These results suggested that different soil microbes can respond differently to altitude. This study provides a novel insight into factors driving rhizosphere soil bacterial and fungal community variations, which could improve our understanding of microbial ecology in alpine R. nitidulum shrub ecosystems along altitude.
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Affiliation(s)
- Lulu Xie
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Wanting Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, PR China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Xueyong Pang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, PR China
| | - Qinghua Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, PR China
| | - Chunying Yin
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu 610041, PR China.
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48
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Mushtaq H, Ganai BA, Jehangir A. Exploring soil bacterial diversity in different micro-vegetational habitats of Dachigam National Park in North-western Himalaya. Sci Rep 2023; 13:3090. [PMID: 36813837 PMCID: PMC9947166 DOI: 10.1038/s41598-023-30187-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Dachigam National Park (DNP), in Zabarwan mountains of north-western Himalaya constitutes a region of high biodiversity with greater endemism. DNP is known for its unique micro-climate together with distinct vegetational zones providing home to variety of threatened and endemic plant, animal, and bird species. However, studies on soil microbial diversity in fragile ecosystems of north-western Himalaya in general and DNP in particular are lacking. This was thus a maiden attempt to study variations in soil bacterial diversity of DNP with respect to changing soil physico-chemical properties, vegetation, and altitude. Soil parameters depicted significant variations among different sites with highest values for temperature, OC, OM and TN being 22.2 ± 0.75 °C, 6.53 ± 0.32%, 11.25 ± 0.54%, 0.545 ± 0.04% from site-2 (low altitudinal grassland site) in summer and lowest of 5.1 ± 0.65 °C, 1.24 ± 0.26%, 2.14 ± 0.45% and 0.132 ± 0.04% at site-9 (high altitudinal mixed pine site) in winter. Bacterial CFU showed significant correlations with soil physico-chemical attributes. This study led to the isolation and identification of 92 morphologically varied bacteria with the highest (15) from site-2 and lowest (04) from site-9 which post BLAST analysis (via 16S rRNA analysis) depicted presence of only 57 distinct bacterial species under taxonomic phylum, Firmicutes and Proteobacteria. Nine species were widely spread (i.e., isolated from > 3 sites), however, most bacteria (37) were restricted to a particular site. Diversity indices ranged between 1.380 to 2.631 (Shannon-Weiner's index); 0.747 to 0.923 (Simpson's index) with highest values for site-2 and lowest for site-9. Index of similarity was highest (47.1%) between riverine sites (site-3 and site-4) whereas two mixed pine sites (site-9 and site-10) showed no similarity.
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Affiliation(s)
- Hina Mushtaq
- grid.412997.00000 0001 2294 5433Terrestrial Ecology Laboratory, Department of Environmental Science, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir 190006 India
| | - Bashir Ahmad Ganai
- grid.412997.00000 0001 2294 5433Centre of Research for Development, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir 190006 India
| | - Arshid Jehangir
- Terrestrial Ecology Laboratory, Department of Environmental Science, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190006, India.
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49
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Ghare U, Narvekar S, Lodha T, Mallebhari R, Dastager S, Barvkar VT, Dhotre D, Karmalkar NR, Pable AA. Bacterial Communities and Diversity of Western Ghats Soil: A Study of a Biodiversity Hotspot. Curr Microbiol 2023; 80:108. [PMID: 36807001 DOI: 10.1007/s00284-023-03207-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/31/2023] [Indexed: 02/19/2023]
Abstract
The Western Ghats is one of India's mega-diversity hotspots and an ecologically and geologically important area for the diversity of endemic plants and animals. The present study provides insights into the aerobic bacterial diversity and composition of the soils of North Western Ghats located in Maharashtra state (NWGM), India. The samples for the culture-dependent study were collected from 6 different locations namely Malshej Ghat, Bhimashankar, Lonavala, Mulshi, Tail-Baila, and Mahabaleshwar. A total of 173 isolates were obtained from the different samples, which belonged to Proteobacteria (43%), Firmicutes (36%), and Actinobacteria (19%). Sequences of 15 strains shared ≤ 98.7% similarity (a species cut-off) which represent potential novel species. Metagenomic analysis revealed the presence of Actinobacteria and Proteobacteria as the most dominant phyla at both MB and MG. However, both sites showed variation in the composition of rare phyla and other dominant phyla. This difference in bacterial community composition could be due to differences in altitude or other physicochemical properties. The functional prediction from the amplicon sequencing showed the abundance of carbohydrate, protein, and lipid metabolism which was corroborated by screening the isolated bacterial strains for the same. The present study has a unique take on microbial diversity and defines the importance of community assembly processes such as drift, dispersal, and selection. Such processes are relatively important in controlling community diversity, distribution, as well as succession. This study has shown that the microbial community of NWGM is a rich source of polysaccharide degrading bacteria having biotechnological potential.
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Affiliation(s)
- Uma Ghare
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Simran Narvekar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Tushar Lodha
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Rubiya Mallebhari
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Syed Dastager
- National Collection of Industrial Microorganisms (NCIM), National Chemical Laboratory, Pune, India
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | | | | | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.
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Distinct Responses of Abundant and Rare Soil Bacteria to Nitrogen Addition in Tropical Forest Soils. Microbiol Spectr 2023; 11:e0300322. [PMID: 36622236 PMCID: PMC9927163 DOI: 10.1128/spectrum.03003-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Soil microbial responses to anthropogenic nitrogen (N) enrichment at the overall community level has been extensively studied. However, the responses of community dynamics and assembly processes of the abundant versus rare bacterial taxa to N enrichment have rarely been assessed. Here, we present a study in which the effects of short- (2 years) and long-term (13 years) N additions to two nearby tropical forest sites on abundant and rare soil bacterial community composition and assembly were documented. The N addition, particularly in the long-term experiment, significantly decreased the bacterial α-diversity and shifted the community composition toward copiotrophic and N-sensitive species. The α-diversity and community composition of the rare taxa were more affected, and they were more closely clustered phylogenetically under N addition compared to the abundant taxa, suggesting the community assembly of the rare taxa was more governed by deterministic processes (e.g., environmental filtering). In contrast, the abundant taxa exhibited higher community abundance, broader environmental thresholds, and stronger phylogenetic signals under environmental changes than the rare taxa. Overall, these findings illustrate that the abundant and rare bacterial taxa respond distinctly to N addition in tropical forests, with higher sensitivity of the rare taxa, but potentially broader environmental acclimation of the abundant taxa. IMPORTANCE Atmospheric nitrogen (N) deposition is a worldwide environmental problem and threatens biodiversity and ecosystem functioning. Understanding the responses of community dynamics and assembly processes of abundant and rare soil bacterial taxa to anthropogenic N enrichment is vital for the management of N-polluted forest soils. Our sequence-based data revealed distinct responses in bacterial diversity, community composition, environmental acclimation, and assembly processes between abundant and rare taxa under N-addition soils in tropical forests. These findings provide new insight into the formation and maintenance of bacterial diversity and offer a way to better predict bacterial responses to the ongoing atmospheric N deposition in tropical forests.
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