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Susanti WI, Krashevska V, Widyastuti R, Stiegler C, Gunawan D, Scheu S, Potapov AM. Seasonal fluctuations of litter and soil Collembola and their drivers in rainforest and plantation systems. PeerJ 2024; 12:e17125. [PMID: 38577414 PMCID: PMC10993886 DOI: 10.7717/peerj.17125] [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: 09/26/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024] Open
Abstract
Rainforest conversion and expansion of plantations in tropical regions change local microclimate and are associated with biodiversity decline. Tropical soils are a hotspot of animal biodiversity and may sensitively respond to microclimate changes, but these responses remain unexplored. To address this knowledge gap, here we investigated seasonal fluctuations in density and community composition of Collembola, a dominant group of soil invertebrates, in rainforest, and in rubber and oil palm plantations in Jambi province (Sumatra, Indonesia). Across land-use systems, the density of Collembola in the litter was at a maximum at the beginning of the wet season, whereas in soil it generally varied little. The community composition of Collembola changed with season and the differences between land-use systems were most pronounced at the beginning of the dry season. Water content, pH, fungal and bacterial biomarkers, C/N ratio and root biomass were identified as factors related to seasonal variations in species composition of Collembola across different land-use systems. We conclude that (1) conversion of rainforest into plantation systems aggravates detrimental effects of low moisture during the dry season on soil invertebrate communities; (2) Collembola communities are driven by common environmental factors across land-use systems, with water content, pH and food availability being most important; (3) Collembola in litter are more sensitive to climatic variations than those in soil. Overall, the results document the sensitivity of tropical soil invertebrate communities to seasonal climatic variations, which intensifies the effects of the conversion of rainforest into plantation systems on soil biodiversity.
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Affiliation(s)
- Winda Ika Susanti
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg-August Universität Göttingen, Göttingen, Germany
| | - Valentyna Krashevska
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg-August Universität Göttingen, Göttingen, Germany
| | - Rahayu Widyastuti
- Department of Soil Sciences and Land Resources, Bogor Institute of Agriculture, Bogor, Indonesia
| | | | - Dodo Gunawan
- Center for Climate Change Information, Agency for Meteorology Climatology and Geophysics, Jakarta, Indonesia
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg-August Universität Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use, Göttingen, Germany
| | - Anton M. Potapov
- J.F. Blumenbach Institute of Zoology and Anthropology, Georg-August Universität Göttingen, Göttingen, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Institute of Biology, University of Leipzig, Leipzig, Germany
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2
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Smenderovac E, Emilson C, Rheault K, Brazeau É, Morency MJ, Gagné P, Venier L, Martineau C. Drying as an effective method to store soil samples for DNA-based microbial community analyses: a comparative study. Sci Rep 2024; 14:1725. [PMID: 38242898 PMCID: PMC10798986 DOI: 10.1038/s41598-023-50541-2] [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: 06/29/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024] Open
Abstract
Soil sampling for environmental DNA in remote and semi-remote locations is often limited due to logistical constraints surrounding sample preservation, including no or limited access to a freezer. Freezing at - 20 °C is a common DNA preservation strategy, however, other methods such as desiccation, ethanol or commercial preservatives are available as potential alternative DNA preservation methods for room temperature storage. In this study, we assessed five preservation methods (CD1 solution, 95% Ethanol, Dry & Dry silica gel packs, RNAlater, LifeGuard) along with freezing at - 20 °C, against immediate extraction on organic and mineral soils for up to three weeks of preservation. We assessed direct effects on DNA concentration and quality, and used DNA metabarcoding to assess effects on bacterial and fungal communities. Drying with Dry & Dry led to no significant differences from immediate extraction. RNAlater led to lower DNA concentrations, but effects on community structures were comparable to freezing. CD1, LifeGuard and Ethanol either caused immediate significant shifts in community structure, degradation of DNA quality or changes in diversity metrics. Overall, our study supports the use of drying with silica gel packs as a cost-effective, and easily applied method for the short-term storage at room temperature for DNA-based microbial community analyses.
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Affiliation(s)
| | - Caroline Emilson
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
| | - Karelle Rheault
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
| | - Élodie Brazeau
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
| | | | - Patrick Gagné
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
| | - Lisa Venier
- Canadian Forest Service, Natural Resources Canada, Ottawa, Canada
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He K, Liu Q, Zhang J, Zhang G, Li G. Biochar Enhances the Resistance of Legumes and Soil Microbes to Extreme Short-Term Drought. PLANTS (BASEL, SWITZERLAND) 2023; 12:4155. [PMID: 38140481 PMCID: PMC10748378 DOI: 10.3390/plants12244155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
Short-term drought events occur more frequently and more intensively under global climate change. Biochar amendment has been documented to ameliorate the negative effects of water deficits on plant performance. Moreover, biochar can alter the soil microbial community, soil properties and soil metabolome, resulting in changes in soil functioning. We aim to reveal the extent of biochar addition on soil nutrients and the soil microbial community structure and how this improves the tolerance of legume crops (peanuts) to short-term extreme drought. We measured plant performances under different contents of biochar, set as a gradient of 2%, 3% and 4%, after an extreme experimental drought. In addition, we investigated how soil bacteria and fungi respond to biochar additions and how the soil metabolome changes in response to biochar amendments, with combined growth experiments, high-throughput sequencing and soil omics. The results indicated that biochar increased nitrites and available phosphorus. Biochar was found to influence the soil bacterial community structure more intensively than the soil fungal community. Additionally, the fungal community showed a higher randomness under biochar addition when experiencing short-term extreme drought compared to the bacterial community. Soil bacteria may be more strongly related to soil nutrient cycling in peanut agricultural systems. Although the soil metabolome has been documented to be influenced by biochar addition independent of soil moisture, we found more differential metabolites with a higher biochar content. We suggest that biochar enhances the resistance of plants and soil microbes to short-term extreme drought by indirectly modifying soil functioning probably due to direct changes in soil moisture and soil pH.
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Affiliation(s)
- Kang He
- Shandong Peanut Research Institute, Qingdao 266100, China;
| | - Qiangbo Liu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an 271018, China;
| | - Jialei Zhang
- Shandong Academy of Agricultural Sciences, Jinan 250100, China;
| | - Guanchu Zhang
- Shandong Peanut Research Institute, Qingdao 266100, China;
| | - Guolin Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-Sen University, Shenzhen 518107, China
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4
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Lee JH, Lee JY, Kang YG, Kim JH, Oh TK. Evaluating methane emissions from rice paddies: A study on the cultivar and transplanting date. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166174. [PMID: 37562609 DOI: 10.1016/j.scitotenv.2023.166174] [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: 05/11/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
Climate change, driven by increased greenhouse gas emissions, is a pressing environmental issue worldwide. Flooded rice paddy soils are a predominant source of methane (CH4) emissions, accounting for approximately 11 % of global emissions. Factors such as rice (Oryza sativa L.) cultivar, transplanting date, water management, and soil characteristics significantly influence these emissions. This study aimed to evaluate the CH4 emissions from rice paddies in relation to the cultivar and transplanting date. The experiment included two rice cultivars (an early-maturing cultivar, Unkwang, and a medium-late-maturing cultivar, Samkwang) and four transplanting dates (Times 1-4). In the present study, CH4 emissions were higher with earlier transplanting dates and decreased significantly with delayed transplanting. Weather conditions, such as cumulative mean air temperature, cumulative soil temperature, and total sunshine hours, were positively correlated with total CH4 emissions. The recommended regional transplanting date (Time 3) resulted in the highest rice grain yields for both cultivars. However, the earlier transplanting dates (Time 1 and Time 2) were more effective in improving plant growth characteristics such as rice straw weight, root biomass weight, and chlorophyll content. A significant positive correlation was observed between the root biomass weight of the rice and CH4 emissions in both cultivars, implying that an increase in root biomass weight led to an increase in CH4 emissions. Consequently, adhering to the advised regional transplanting dates is the most sensible approach for transplanting rice seedlings. This ensured lower CH4 emissions without compromising rice productivity or quality for both cultivars. Further research should focus on identifying the most appropriate rice-transplanting dates and management practices to effectively reduce CH4 emissions without compromising rice production.
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Affiliation(s)
- Jae-Han Lee
- Department of Bio-Environmental Chemistry, Chungnam National University, Daejeon 34134, South Korea
| | - Jun-Yeong Lee
- Department of Bio-Environmental Chemistry, Chungnam National University, Daejeon 34134, South Korea
| | - Yun-Gu Kang
- Department of Bio-Environmental Chemistry, Chungnam National University, Daejeon 34134, South Korea
| | - Jun-Ho Kim
- Department of Bio-Environmental Chemistry, Chungnam National University, Daejeon 34134, South Korea
| | - Taek-Keun Oh
- Department of Bio-Environmental Chemistry, Chungnam National University, Daejeon 34134, South Korea.
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Santos-Medellín C, Blazewicz SJ, Pett-Ridge J, Firestone MK, Emerson JB. Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils. Nat Ecol Evol 2023; 7:1809-1822. [PMID: 37770548 DOI: 10.1038/s41559-023-02207-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 08/25/2023] [Indexed: 09/30/2023]
Abstract
As central members of soil trophic networks, viruses have the potential to drive substantial microbial mortality and nutrient turnover. Pinpointing viral contributions to terrestrial ecosystem processes remains a challenge, as temporal dynamics are difficult to unravel in the spatially and physicochemically heterogeneous soil environment. In Mediterranean grasslands, the first rainfall after seasonal drought provides an ecosystem reset, triggering microbial activity during a tractable window for capturing short-term dynamics. Here, we simulated precipitation in microcosms from four distinct dry grassland soils and generated 144 viromes, 84 metagenomes and 84 16S ribosomal RNA gene amplicon datasets to characterize viral, prokaryotic and relic DNA dynamics over 10 days. Vastly different viral communities in each soil followed remarkably similar successional trajectories. Wet-up triggered a significant increase in viral richness, followed by extensive compositional turnover. Temporal succession in prokaryotic communities was much less pronounced, perhaps suggesting differences in the scales of activity captured by viromes (representing recently produced, ephemeral viral particles) and total DNA. Still, differences in the relative abundances of Actinobacteria (enriched in dry soils) and Proteobacteria (enriched in wetted soils) matched those of their predicted phages, indicating viral predation of dominant bacterial taxa. Rewetting also rapidly depleted relic DNA, which subsequently reaccumulated, indicating substantial new microbial mortality in the days after wet-up, particularly of the taxa putatively under phage predation. Production of abundant, diverse viral particles via microbial host cell lysis appears to be a conserved feature of the early response to soil rewetting, and results suggest the potential for 'Cull-the-Winner' dynamics, whereby viruses infect and cull but do not decimate dominant host populations.
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Affiliation(s)
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California, Merced, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA.
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6
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Xiao Y, Bao F, Xu X, Yu K, Wu B, Gao Y, Zhang J. The influence of precipitation timing and amount on soil microbial community in a temperate desert ecosystem. Front Microbiol 2023; 14:1249036. [PMID: 37744930 PMCID: PMC10512721 DOI: 10.3389/fmicb.2023.1249036] [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: 06/28/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction Global climate change may lead to changes in precipitation patterns. This may have a significant impact on the microbial communities present in the soil. However, the way these communities respond to seasonal variations in precipitation, particularly in the context of increased precipitation amounts, is not yet well understood. Methods To explore this issue, a five-year (2012-2016) field study was conducted at the northeast boundary of the Ulan Buh Desert, examining the effects of increased precipitation during different periods of the growing season on both bacterial and fungal communities. The study included five precipitation pattern treatments: a control group (C), as well as groups receiving 50 and 100% of the local mean annual precipitation amount (145 mm) during either the early growing season (E50 and E100) or the late growing season (L50 and L100). The taxonomic composition of the soil bacterial and fungal communities was analyzed using Illumina sequencing. Results After 5 years, the bacterial community composition had significantly changed in all treatment groups, with soil bacteria proving to be more sensitive to changes in precipitation timing than to increased precipitation amounts within the desert ecosystem. Specifically, the alpha diversity of bacterial communities in the late growing season plots (L50 and L100) decreased significantly, while no significant changes were observed in the early growing season plots (E50 and E100). In contrast, fungal community composition remained relatively stable in response to changes in precipitation patterns. Predictions of bacterial community function suggested that the potential functional taxa in the bacterial community associated with the cycling of carbon and nitrogen were significantly altered in the late growing season (L50 and L100). Discussion These findings emphasize the importance of precipitation timing in regulating microbial communities and ecosystem functions in arid regions experiencing increased precipitation amounts.
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Affiliation(s)
- Yao Xiao
- Key Laboratory of Forest Disaster Warning and Control in Yunnan Province, Faculty of Biodiversity Conservation, Southwest Forestry University, Kunming, China
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Fang Bao
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Xiaotian Xu
- Beijing Academy of Forestry and Pomology Sciences, Beijing, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Bo Wu
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Ying Gao
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Junzhong Zhang
- Key Laboratory of Forest Disaster Warning and Control in Yunnan Province, Faculty of Biodiversity Conservation, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming, China
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7
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Zhang H, Zhang M, Hou X, Li Y, Zhang W, Wang L, Niu L. Responses of bacterial community and N-cycling functions stability to different wetting-drying alternation frequencies in a riparian zone. ENVIRONMENTAL RESEARCH 2023; 228:115778. [PMID: 36997041 DOI: 10.1016/j.envres.2023.115778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 05/16/2023]
Abstract
Wetting-drying alternation (WD) of the soil is one of the key characteristics of riparian zones shaped by dam construction, profoundly impacting the soil microenvironment that determines the bacterial community. Knowledge concerning the stability of bacterial community and N-cycling functions in response to different frequencies of WD remains unclear. In this study, samples were taken from a riparian zone in the Three Gorges Reservoir (TGR) and an incubation experiment was conducted including four treatments: constant flooding (W), varied wetting-drying alternation frequencies (WD1 and WD2), and constant drying (D) (simulating water level of 145 m, 155 m, 165 m, and 175 m in the riparian zone respectively). The results revealed that there was no significant difference in the diversity among the four treatments. Following the WD1 and WD2 treatments, the relative abundances of Proteobacteria increased, while those of Chloroflexi and Acidobacteriota decreased compared to the W treatment. However, the stability of bacterial community was not affected by WD. Relative to the W treatment, the stability of N-cycling functions estimated by resistance, which refers to the ability of functional genes to adapt to changes in the environment, decreased following the WD1 treatment, but showed no significant change following the WD2 treatment. Random forest analysis showed that the resistances of the nirS and hzo genes were core contributors to the stability of N-cycling functions. This study provides a new perspective for investigating the impacts of wetting-drying alternation on soil microbes.
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Affiliation(s)
- Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Mengzhu Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Xing Hou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
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Zhu K, Jia W, Mei Y, Wu S, Huang P. Shift from flooding to drying enhances the respiration of soil aggregates by changing microbial community composition and keystone taxa. Front Microbiol 2023; 14:1167353. [PMID: 37250047 PMCID: PMC10214030 DOI: 10.3389/fmicb.2023.1167353] [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: 02/16/2023] [Accepted: 04/19/2023] [Indexed: 05/31/2023] Open
Abstract
Changes in the water regime are among the crucial factors controlling soil carbon dynamics. However, at the aggregate scale, the microbial mechanisms that regulate soil respiration under flooding and drying conditions are obscure. In this research, we investigated how the shift from flooding to drying changes the microbial respiration of soil aggregates by affecting microbial community composition and their co-occurrence patterns. Soils collected from a riparian zone of the Three Gorges Reservoir, China, were subjected to a wet-and-dry incubation experiment. Our data illustrated that the shift from flooding to drying substantially enhanced soil respiration for all sizes of aggregate fractions. Moreover, soil respiration declined with aggregate size in both flooding and drying treatments. The keystone taxa in bacterial networks were found to be Acidobacteriales, Gemmatimonadales, Anaerolineales, and Cytophagales during the flooding treatment, and Rhizobiales, Gemmatimonadales, Sphingomonadales, and Solirubrobacterales during the drying treatment. For fungal networks, Hypocreales and Agaricalesin were the keystone taxa in the flooding and drying treatments, respectively. Furthermore, the shift from flooding to drying enhanced the microbial respiration of soil aggregates by changing keystone taxa. Notably, fungal community composition and network properties dominated the changes in the microbial respiration of soil aggregates during the shift from flooding to drying. Thus, our study highlighted that the shift from flooding to drying changes keystone taxa, hence increasing aggregate-scale soil respiration.
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Retter A, Haas JC, Birk S, Stumpp C, Hausmann B, Griebler C, Karwautz C. From the Mountain to the Valley: Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor. Microorganisms 2023; 11:microorganisms11030779. [PMID: 36985351 PMCID: PMC10055094 DOI: 10.3390/microorganisms11030779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/08/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023] Open
Abstract
Rivers are the “tip of the iceberg”, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.
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Affiliation(s)
- Alice Retter
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
| | | | - Steffen Birk
- Institute of Earth Sciences, NAWI Graz Geocenter, University of Graz, 8010 Graz, Austria
| | - Christine Stumpp
- Institute of Soil Physics and Rural Water Management, University of Natural Resources and Life Sciences (BOKU), 1180 Wien, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Wien, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Wien, Austria
| | - Christian Griebler
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
| | - Clemens Karwautz
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
- Correspondence:
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10
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Du Y, Wang YP, Hui D, Su F, Yan J. Significant effects of precipitation frequency on soil respiration and its components-A global synthesis. GLOBAL CHANGE BIOLOGY 2023; 29:1188-1205. [PMID: 36408676 DOI: 10.1111/gcb.16532] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Global warming intensifies the hydrological cycle, which results in changes in precipitation regime (frequency and amount), and will likely have significant impacts on soil respiration (Rs ). Although the responses of Rs to changes in precipitation amount have been extensively studied, there is little consensus on how Rs will be affected by changes in precipitation frequency (PF) across the globe. Here, we synthesized the field observations from 296 published papers to quantify the effects of PF on Rs and its components using meta-analysis. Our results indicated that the effects of PF on Rs decreased with an increase in background mean annual precipitation. When the data were grouped by climate conditions, increased PF showed positive effects on Rs under the arid condition but not under the semi-humid or humid conditions, whereas decreased PF suppressed Rs across all the climate conditions. The positive effects of increased PF mainly resulted from the positive response of heterotrophic respiration under the arid condition while the negative effects of decreased PF were mainly attributed to the reductions in root biomass and respiration. Overall, our global synthesis provided for the first time a comprehensive analysis of the divergent effects of PF on Rs and its components across climate regions. This study also provided a framework for understanding and modeling responses of ecosystem carbon cycling to global precipitation change.
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Affiliation(s)
- Yue Du
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Geography and Environmental Science, Henan University, Kaifeng, China
| | - Ying-Ping Wang
- CSIRO Oceans and Atmosphere, Aspendale, Victoria, Australia
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, Nashville, Tennessee, USA
| | - Fanglong Su
- School of Life Sciences, Henan University, Kaifeng, China
| | - Junhua Yan
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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11
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Shen Q, Zhang K, Voroney P, Meng L, Xu J, Brookes P. Biodiesel Co-Product enhances microbial stability and beneficial microbial communities along a gradient of soil water content. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159204. [PMID: 36198351 DOI: 10.1016/j.scitotenv.2022.159204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Biodiesel Co-Product (BCP) is a complex carbonaceous liquid formed during the commercial production of biodiesel. Previously, BCP was shown to decrease nitrogen (N) leaching from the soil, but the effects of BCP on the diversity, composition, and structure of soil microbial communities are not well understood. Here, we applied 1.5 mg BCP-C to acidic soil (pH 3.5) at a range of different water contents (from 40 % to 100 % water holding capacity) to investigate the interactions between BCP and increasing water holding capacity on the diversity, composition, and interactions of soil microbial communities. Distance-based multivariate linear model (DistLM) and non-metric multidimensional scaling (NMDS) analyses showed that BCP caused larger changes in fungal than bacterial communities, while soil water content had a greater effect on bacterial communities relative to fungal communities. Co-occurrence network analyses indicated that BCP amendment produced more robust and complex bacterial networks and more stable fungal ones. BCP significantly increased the OTU numbers of beneficial microbes (e.g., Trichoderma spp.) in all water contents, with fewer OTU numbers of putative pathogenetic species (Fusarium spp. and Aspergillus spp.). These findings indicate that BCP addition may be conducive to the health and stability of soil ecosystems.
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Affiliation(s)
- Qunli Shen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Faculty of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Kaile Zhang
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA; Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, USA.
| | - Paul Voroney
- Faculty of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Lei Meng
- School of Tropical Crops, Hainan University, Haikou 570228, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Philip Brookes
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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Zhou J, Jia R, Brown RW, Yang Y, Zeng Z, Jones DL, Zang H. The long-term uncertainty of biodegradable mulch film residues and associated microplastics pollution on plant-soil health. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130055. [PMID: 36303333 DOI: 10.1016/j.jhazmat.2022.130055] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/15/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Biodegradable mulch film potentially offers an encouraging alternative to conventional (petroleum-based) plastic films. Since biodegradable films are more susceptible to rapid degradation, more microplastics (MPs) are likely to be generated than conventional films within the same time frame, probably leading to more severe MPs pollution and associated effects. However, the effect of biodegradable mulch film residues and associated MPs pollution on plant-soil health remains uncertainty. Here, we evaluated the potential effect of bio-MPs pollution on soil carbon (C) and nutrient (i.e., N and P) cycling, soil biology (microorganisms and mesofauna), and plant health, as these are crucial to agroecosystem functioning and the delivery of key ecosystem services. Unlike the inert (and therefore recalcitrant) C contained within petroleum-based MPs, at least 80% of the C from bio-MPs is converted to CO2, with up to 20% immobilized in living microbial biomass (i.e., < 0.05 t C ha-1). Although biodegradable films are unlikely to be important in promoting soil C storage, they may accelerate microbial biomass turnover in the short term, as well as CO2 production. Compared to conventional MPs, bio-MPs degradation is more pronounced, thereby inducing greater alterations in microbial diversity and community composition. This may further alter N2O and CH4 emissions, and ultimately resulting in unpredictable consequences for global climate warming. The extent to which this may occur, however, has yet to be shown in either laboratory or field studies. In addition, bio-MPs have a large chance of forming nanoplastics, potentially causing a stronger toxic effect on plants relative to conventional MPs. Consequently, this would influence plant health, crop productivity, and food safety, leading to potential health risks. It is unclear, however, if these are direct effects on key plant processes (e.g. signaling, cell expansion) or indirect effects (e.g. nutrient deficiency or acidification). Overall, the question as to whether biodegradable mulch films offer a promising alternative to solve the conventional plastic legacy in soil over the long term remains unclear.
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Affiliation(s)
- Jie Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Rong Jia
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Robert W Brown
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Yadong Yang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhaohai Zeng
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK; SoilsWest, Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA 6105, Australia
| | - Huadong Zang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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Jin X, Wu F, Wu Q, Heděnec P, Peng Y, Wang Z, Yue K. Effects of drying-rewetting cycles on the fluxes of soil greenhouse gases. Heliyon 2023; 9:e12984. [PMID: 36704269 PMCID: PMC9871208 DOI: 10.1016/j.heliyon.2023.e12984] [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: 01/02/2023] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Irregular precipitation caused by climate changes has resulted in frequent events of soil drying-rewetting cycles (DWC), which can strongly affect soil carbon (C) and nitrogen (N) cycling, including the fluxes of greenhouse gases (GHGs). The response of soil carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) fluxes to DWC events may differ among different ecosystem types and vary with experimental settings and soil properties, but these processes were not quantitatively assessed. Here, we evaluated the responses of soil GHG fluxes to DWC, compared with consistent moisture, as well as the associated driving factors with 424 paired observations collected from 47 publications of lab incubation experiments. Results showed that: (1) DWC significantly decreased soil CO2 emissions by an average of 9.7%, but did not affect the emissions and uptakes of soil CH4 and N2O; (2) DWC effects on soil GHG emissions varied significantly among different ecosystem types, with CO2 emissions significantly decreased by 6.8 and 16.3% in croplands and grasslands soils, respectively, and CH4 and N2O emissions significantly decreased and increased in wetlands and forests soils, respectively; (3) the effects of DWC on CO2 emissions were also positively regulated by organic C and N concentrations, pH, clay concentration, and soil depth, but negatively by C:N ratio and silt concentration, while DWC effects on N2O emissions were negatively controlled by C:N ratio, silt concentration, and soil depth. Overall, our results showed that CO2 emissions were significantly decreased by DWC, while the fluxes of CH4 and N2O were not affected, indicating an overall decrease of GHGs in response to DWC. Our results will be useful for a better understanding of global GHG emissions under future climate change scenario.
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Affiliation(s)
- Xia Jin
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Fuzhong Wu
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China,Fujian Sanming Forest Ecosystem National Observation and Research Station, Sanming 365002, China
| | - Qiqian Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an 311300, China
| | - Petr Heděnec
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, 21030, Terengganu, Malaysia
| | - Yan Peng
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Zheng Wang
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Kai Yue
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China,Fujian Sanming Forest Ecosystem National Observation and Research Station, Sanming 365002, China,Corresponding author. Wulongjiang Middle Avenue 18, Shangjie Town, Minhou County, Fuzhou 350117, Fujian, China.
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14
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Jia W, Wang S, He X, Zhao X. Different factors drive the assembly of pine and Panax notoginseng-associated microbiomes in Panax notoginseng-pine agroforestry systems. Front Microbiol 2022; 13:1018989. [DOI: 10.3389/fmicb.2022.1018989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/24/2022] [Indexed: 11/15/2022] Open
Abstract
Land-use conversion affects the composition and assembly of plant-associated microbiomes, which in turn affects plant growth, development, and ecosystem functioning. However, agroforestry systems, as sustainable land types, have received little attention regarding the dynamics of different plant-associated microbes. In this study, we used high-throughput sequencing technology to analyze the assembly mechanisms and the driving factors of pine- and Panax notoginseng (P.n.)-associated microbiomes during the conversion of different pine forests (Pinus kesiya var. langbianensis and Pinus armandii) into P.n.-pine agroforestry systems. The results showed that the conversion of pure pine forest into P.n.-pine agroforestry systems significantly altered the diversity of pine-associated fungi rather than the community structure, and the community structure of P.n.-associated fungi rather than the diversity. Additionally, plant-associated fungi were more responsive to land-use change than bacteria. Main effect analysis revealed that compartment rather than genotype was the driving factor of pine- and P.n.-associated microbiomes, but P.n. cultivation also significantly affected the assembly of pine-associated microbiomes. In addition, there was a transfer of P.n. endophytes to pine trees in agroforestry systems and the beneficial microbiomes (Massilia, Marmoricola, Herbaspirillum, etc.) were enlarged in pine roots. Therefore, the diversity of the assembly mechanisms of P.n.- and pine-associated microbiomes played an important role in the P.n.--pine agroforestry systems and were the basis for the sustainable development of the P.n.--pine agroforestry systems.
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15
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Ouverson T, Boss D, Eberly J, Seipel T, Menalled FD, Ishaq SL. Soil bacterial community response to cover crops, cover crop termination, and predicted climate conditions in a dryland cropping system. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.911199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Soil microbial communities are integral to highly complex soil environments, responding to changes in aboveground plant biodiversity, influencing physical soil structure, driving nutrient cycling, and promoting both plant growth and disease suppression. Cover crops can improve soil health, but little is known about their effects on soil microbial community composition in semiarid cropping systems, which are rapidly becoming warmer and drier due to climate change. This study focused on a wheat-cover crop rotation near Havre, Montana that tested two cover crop mixtures (five species planted early season and seven species planted mid-season) with three different termination methods (chemical, grazed, or hayed and baled) against a fallow control under ambient or induced warmer/drier conditions. Soil samples from the 2018 and 2019 cover crop/fallow phases were collected for bacterial community 16S rRNA gene sequencing. The presence and composition of cover crops affected evenness and community composition. Bacterial communities in the 2018 ambient mid-season cover crops, warmer/drier mid-season cover crops, and ambient early season cover crops had greater richness and diversity than those in the warmer/drier early season cover crops. Soil microbial communities from mid-season cover crops were distinct from the early season cover crops and fallow. No treatments affected bacterial alpha or beta diversity in 2019, which could be attributed to high rainfall. Results indicate that cover crop mixtures including species tolerant to warmer and drier conditions can foster diverse soil bacterial communities compared to fallow soils.
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16
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Chai X, Xu X, Li L, Wang W, Li S, Geming P, Qu Y, Zhang Q, Ren X, Xu Y, Li M. Physicochemical and biological factors determining the patchy distribution of soil water repellency among species of dominant vegetation in loess hilly region of China. FRONTIERS IN PLANT SCIENCE 2022; 13:908035. [PMID: 36275577 PMCID: PMC9582861 DOI: 10.3389/fpls.2022.908035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Soil water repellency (SWR) is a physical phenomenon whereby water cannot penetrate or has difficulty penetrating the soil surface. There are many factors involved in its occurrence, but the main factors controlling its emergence in loess remain unclear. In this work, we have studied numerous physicochemical and biological factors functioning in different dominant vegetations (Pinus tabulaeformis Carr., Robinia pseudoacacia L., and Hippophae rhamnoides L.) in a loess hilly region by gas chromatography-mass spectrometry (GC-MS) and high-throughput sequencing techniques. We observed that more than 75% of the soils under Robinia and Hippophae are categorized as slightly or strongly water repellent, while nearly 50% of the soils under Pinus are categorized as severely to extremely water repellent. The relative concentrations of total free lipids in the soil in the same water-repellency class were Pinus > Robinia > Hippophae, where fatty acids, alkanols, and sterols were positively correlated with SWR, whereas alkanes were not. For the abundance and diversity index of bacterial and fungal communities, the three species ranked in the following order: Robinia ≈ Hippophae > Pinus. Thus, solvent-extractable polar waxes were indicated to be better preserved in water-repellent soils under Pinus due to lower microbial diversity than Robinia and Hippophae. Here, we demonstrate polar waxes to be the principal factor controlling SWR. Moreover, the dominant phyla of fungi varied greatly than those of bacteria under three vegetation types. Correlation analysis showed that the abundance of Actinobacteria in dominant bacteria increased with SWR. Nonmetric multidimensional scaling suggested the fungal community in different water-repellent soils under Pinus to vary more than those under Robinia and Hippophae. The indicator species mainly belonged to Actinobacteria in bacteria and Basidiomycota in fungi at the phylum level; this finding was further supported by the linear discriminant analysis (LDA) effect size (LEfSe). Additionally, GC-MS identified a small amount of ergosterol, a specific biomarker of fungi under Pinus. These pieces of evidence collectively reveal that severe to extreme SWR occurs under Pinus and appears to be the most influenced by fungi and actinomycetes when the topsoil is close to air drying. However, there is a need for further testing on different plant species or land use.
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Affiliation(s)
- Xiaohong Chai
- College of Grassland Agriculture, Northwest A & F University, Yangling, China
| | - Xuexuan Xu
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, China
| | - Lushan Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Weiwei Wang
- College of Grassland Agriculture, Northwest A & F University, Yangling, China
| | - Shuo Li
- College of Grassland Agriculture, Northwest A & F University, Yangling, China
| | - Palixiati Geming
- College of Grassland Agriculture, Northwest A & F University, Yangling, China
| | - Yuanyuan Qu
- College of Grassland Agriculture, Northwest A & F University, Yangling, China
| | - Qi Zhang
- College of Grassland Agriculture, Northwest A & F University, Yangling, China
| | - Xiuzi Ren
- College of Grassland Agriculture, Northwest A & F University, Yangling, China
| | - Yuanhui Xu
- College of Grassland Agriculture, Northwest A & F University, Yangling, China
| | - Mengyao Li
- College of Grassland Agriculture, Northwest A & F University, Yangling, China
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17
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Schreckinger J, Mutz M, Mendoza-Lera C. When water returns: Drying history shapes respiration and nutrients release of intermittent river sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155950. [PMID: 35588804 DOI: 10.1016/j.scitotenv.2022.155950] [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: 03/08/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Climate change and anthropogenic water demand have increased the frequency and duration of drying periods across rivers and streams worldwide. However, the biogeochemical processes during the water return in desiccated riverbeds are still unclear. Drying is a complex and diverse process and biogeochemical implications upon flow resumption may depend on attributes of the drying and river sediment characteristics (i.e., organic matter content [OM]). In order to understand the effect of drying duration and intensity on the biogeochemical dynamics following flow resumption, we exposed OM- and non-enriched river sediment from an intermittent river section to three different drying intensities (low: shade and rain; moderate: no shade and rain; high: no shade and no rain), each for three drying durations (10, 30 and 90 days). We determined the sediment-associated microbial respiration and dissolved organic carbon (DOC), ammonium‑nitrogen (NH4-N), nitrate‑nitrogen (NO3-N) and soluble reactive phosphorus (SRP) net release/retention rates of the nine drying treatments in flow-through microcosms over four days past flow resumption. Under the most intense and prolonged drying, non-enriched sediments showed a lag response in respiration on the first day after flow resumption, while all other treatments had either a linear increase or an early pulse in respiration. After 48 h, respiration remained constant, with minor changes in respiration dynamics regardless of the OM content of the sediment and drying attributes. The drying duration and intensity had greater effects on SRP release/retention soon after the flow resumption, while NH4-N and NO3-N release/retention rates were more strongly affected four days later. Our results suggest that drying attributes influence the biogeochemical dynamics more strongly during the first 24 h upon flow resumption. However, neither respiration nor nutrient dynamics recovered within four days to levels of the sediments before drying for any drying treatments. Hence, the atrributes of the drying have considerable implications in rivers biogeochemistry upon flow resumption.
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Affiliation(s)
- José Schreckinger
- Department of Freshwater Conservation, Brandenburg University of Technology Cottbus Senftenberg, Bad Saarow, Germany; Koblenz-Landau University, Institute of Environmental Sciences, Landau, Germany.
| | - Michael Mutz
- Department of Freshwater Conservation, Brandenburg University of Technology Cottbus Senftenberg, Bad Saarow, Germany
| | - Clara Mendoza-Lera
- Koblenz-Landau University, Institute of Environmental Sciences, Landau, Germany
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18
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Sarkar S, Kamke A, Ward K, Rudick AK, Baer SG, Ran Q, Feehan B, Thapa S, Anderson L, Galliart M, Jumpponen A, Johnson L, Lee STM. Bacterial but Not Fungal Rhizosphere Community Composition Differ among Perennial Grass Ecotypes under Abiotic Environmental Stress. Microbiol Spectr 2022; 10:e0239121. [PMID: 35442065 PMCID: PMC9241903 DOI: 10.1128/spectrum.02391-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/01/2022] [Indexed: 11/20/2022] Open
Abstract
Environmental change, especially frequent droughts, is predicted to detrimentally impact the North American perennial grasslands. Consistent dry spells will affect plant communities as well as their associated rhizobiomes, possibly altering the plant host performance under environmental stress. Therefore, there is a need to understand the impact of drought on the rhizobiome, and how the rhizobiome may modulate host performance and ameliorate its response to drought stress. In this study, we analyzed bacterial and fungal communities in the rhizospheres of three ecotypes (dry, mesic, and wet) of dominant prairie grass, Andropogon gerardii. The ecotypes were established in 2010 in a common garden design and grown for a decade under persistent dry conditions at the arid margin of the species' range in Colby, Kansas. The experiment aimed to answer whether and to what extent do the different ecotypes maintain or recruit distinct rhizobiomes after 10 years in an arid climate. In order to answer this question, we screened the bacterial and fungal rhizobiome profiles of the ecotypes under the arid conditions of western Kansas as a surrogate for future climate environmental stress using 16S rRNA and ITS2 metabarcoding sequencing. Under these conditions, bacterial communities differed compositionally among the A. gerardii ecotypes, whereas the fungal communities did not. The ecotypes were instrumental in driving the differences among bacterial rhizobiomes, as the ecotypes maintained distinct bacterial rhizobiomes even after 10 years at the edge of the host species range. This study will aid us to optimize plant productivity through the use of different ecotypes under future abiotic environmental stress, especially drought. IMPORTANCE In this study, we used a 10-year long reciprocal garden system, and reports that different ecotypes (dry, mesic, and wet) of dominant prairie grass, Andropogon gerardii can maintain or recruit distinct bacterial but not fungal rhizobiomes after 10 years in an arid environment. We used both 16S rRNA and ITS2 amplicons to analyze the bacterial and fungal communities in the rhizospheres of the respective ecotypes. We showed that A. gerardii might regulate the bacterial community to adapt to the arid environment, in which some ecotypes were not adapted to. Our study also suggested a possible tradeoff between the generalist and the specialist bacterial communities in specific environments, which could benefit the plant host. Our study will provide insights into the plant host regulation of the rhizosphere bacterial and fungal communities, especially during frequent drought conditions anticipated in the future.
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Affiliation(s)
- Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Abigail Kamke
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Kaitlyn Ward
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Aoesta K. Rudick
- Kansas Biological Survey & Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
| | - Sara G. Baer
- Kansas Biological Survey & Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - QingHong Ran
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Brandi Feehan
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Shiva Thapa
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Lauren Anderson
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Matthew Galliart
- Department of Biological Sciences, Fort Hays State University, Hays, Kansas, USA
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Loretta Johnson
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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A Drying-Rewetting Cycle Imposes More Important Shifts on Soil Microbial Communities than Does Reduced Precipitation. mSystems 2022; 7:e0024722. [PMID: 35762785 PMCID: PMC9426475 DOI: 10.1128/msystems.00247-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Global changes will result in altered precipitation patterns, among which the increasing frequency of drought events has the highest deleterious potential for agriculture. Soil microbes have shown some promise to help crops adapt to drought events, but it is uncertain how crop-associated microorganisms will respond to altered precipitation patterns. To investigate this matter, we conducted a field experiment where we seeded two wheat cultivars (one resistant to water stress and the other sensitive) that were subjected to four precipitation exclusion (PE) regimes (0%, 25%, 50%, and 75% exclusion). These cultivars were sampled seven times (every 2 weeks, from May to August) within one growing season to investigate short-term microbiome responses to altered precipitation regimes and seasonality using 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. One of the most striking features of the data set was the dramatic shift in microbial community diversity, structure, and composition together with a doubling of the relative abundance of the archaeal ammonia oxidizer genus Nitrososphaera following an important drying-rewetting event. Comparatively small but significant effects of PE and wheat cultivar on microbial community diversity, composition, and structure were observed. Taken together, our results demonstrate an uneven response of microbial taxa to decreasing soil water content, which was dwarfed by drying-rewetting events, to which soil bacteria and archaea were more sensitive than fungi. Importantly, our study showed that an increase in drying-rewetting cycles will cause larger shifts in soil microbial communities than a decrease in total precipitation, suggesting that under climate changes, the distribution of precipitation will be more important than small variations in the total quantity of precipitation. IMPORTANCE Climate change will have a profound effect on the precipitation patterns of global terrestrial ecosystems. Seasonal and interannual uneven distributions of precipitation will lead to increasing frequencies and intensities of extreme drought and rainfall events, which will affect crop productivity and nutrient contents in various agroecosystems. However, we still lack knowledge about the responses of soil microbial communities to reduced precipitation and drying-rewetting events in agroecosystems. Our results demonstrated an uneven response of the soil microbiome and a dramatic shift in microbial community diversity and structure to a significant drying-rewetting event with a large increase in the relative abundance of archaeal ammonia oxidizers. These findings highlight the larger importance of rewetting of dry soils on microbial communities, as compared to decreased precipitation, with potential for changes in the soil nitrogen cycling.
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Chen Y, Chen R, Liu Z, Ren B, Wu Q, Zhang J, Tang Y, Wu Q. Bioretention system mediated by different dry-wet alterations on nitrogen removal: Performance, fate, and microbial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154295. [PMID: 35247404 DOI: 10.1016/j.scitotenv.2022.154295] [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: 10/19/2021] [Revised: 02/07/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
In laboratory experiments, the nitrogen migration and transformation in the stormwater bioretention system under different dry-wet alterations were studied. The removal efficiency showed that nitrogen could be removed efficiently in bioretention system under all dry-wet alterations, and the shorter antecedent dry days (ADDs) (1-5 days) were beneficial to the removal of nitrogen before plants decay, compared to the longer ADDs (7-22 days). Using a new method combined with Hydrus-1D model, water transport was simulated and nitrogen migration in bioretention system was quantified, indicating that NH4+-N was mainly removed in the planting layer, and the removal of NO3--N was occurred in the submerged layer. Fate experiment showed the main fate of the nitrogen was microorganisms (1-5 ADDs) and soil immobilization (7-22 ADDs). Microbial analysis showed that shorter ADDs (1-5 days) were suitable for Firmicutes growth, while Proteobacteria and Actinobacteria accounted for greater abundance under longer ADDs (7-22 days). Canonical correlation analysis (CCA) revealed the relationships between microbial community and environmental factors. Soil moisture content, soil organic matter (SOM), TN (water), root length, and NO3--N (water) were significantly correlated with bacterial community. This work may give new insights into nitrogen migration and transformation, and can provide a reference for the further mechanism study and construction of stormwater bioretention systems.
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Affiliation(s)
- Yao Chen
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China; Engineering Laboratory of Environmental Hydraulic Engineering of Chongqing Municipal Development and Reform Commission, Chongqing Jiaotong University, Chongqing 400074, China
| | - Renyu Chen
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - Zhen Liu
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China; Engineering Laboratory of Environmental Hydraulic Engineering of Chongqing Municipal Development and Reform Commission, Chongqing Jiaotong University, Chongqing 400074, China.
| | - Bangxing Ren
- Environmental Engineering and Science Program, Department of Chemical and Environmental Engineering (ChEE), University of Cincinnati, Cincinnati, OH 45221-0071, USA
| | - Qiong Wu
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - Jian Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China
| | - Yinghui Tang
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| | - Qingyu Wu
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
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21
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Sannino C, Cannone N, D'Alò F, Franzetti A, Gandolfi I, Pittino F, Turchetti B, Mezzasoma A, Zucconi L, Buzzini P, Guglielmin M, Onofri S. Fungal communities in European alpine soils are not affected by short-term in situ simulated warming than bacterial communities. Environ Microbiol 2022; 24:4178-4192. [PMID: 35691701 DOI: 10.1111/1462-2920.16090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/31/2022] [Indexed: 11/27/2022]
Abstract
The impact of global warming on biological communities colonizing European alpine ecosystems was recently studied. Hexagonal open top chambers (OTCs) were used for simulating a short-term in situ warming (estimated around 1°C) in some alpine soils to predict the impact of ongoing climate change on resident microbial communities. Total microbial DNA was extracted from soils collected either inside or outside the OTCs over 3 years of study. Bacterial and fungal rRNA copies were quantified by qPCR. Metabarcoding sequencing of taxonomy target genes was performed (Illumina MiSeq) and processed by bioinformatic tools. Alpha- and beta-diversity were used to evaluate the structure of bacterial and fungal communities. qPCR suggests that, although fluctuations have been observed between soils collected either inside and outside the OTCs, the simulated warming induced a significant (p < 0.05) shift only for bacterial abundance. Likewise, significant (p < 0.05) changes in bacterial community structure were detected in soils collected inside the OTCs, with a clear increase of oligotrophic taxa. On the contrary, fungal diversity of soils collected either inside and outside the OTCs did not exhibit significant (p < 0.05) differences, suggesting that the temperature increase in OTCs compared to ambient conditions was not sufficient to change fungal communities.
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Affiliation(s)
- Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Nicoletta Cannone
- Department of Theoretical and Applied Sciences, Insubria University, Varese, Italy
| | - Federica D'Alò
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milan, Italy
| | - Isabella Gandolfi
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milan, Italy
| | - Francesca Pittino
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milan, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Ambra Mezzasoma
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Mauro Guglielmin
- Department of Theoretical and Applied Sciences, Insubria University, Varese, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
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22
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Yu S, Sayer EJ, Li Z, Mo Q, Wang M, Li Y, Li Y, Xu G, Hu Z, Wang F. Delayed wet season increases soil net N mineralization in a seasonally dry tropical forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153314. [PMID: 35124037 DOI: 10.1016/j.scitotenv.2022.153314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/02/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Seasonal precipitation regime plays a vital role in regulating nutrient dynamics in seasonally dry tropical forests. Present evidence suggests that not only wet season precipitation is increasing in the tropics of South China, but also that the wet season is occurring later. However, it is unclear how nutrient dynamics will respond to the projected precipitation regime changes. We assessed the impacts of altered seasonal precipitation on soil net N mineralization in a secondary tropical forest. Since 2013, by reducing throughfall and/or irrigating experimental plots, we delayed the wet season by two months from April-September to June-November (DW treatment) or increased annual precipitation by 25% in July and August (WW treatment). We measured soil net N mineralization rates and assessed soil microbial communities in January, April, August and November in 2015 and 2017. We found that a wetter wet season did not significantly affect soil microbes or net N mineralization rates, even in the mid-wet season (August) when soil water content in the WW treatment increased significantly. By contrast, a delayed wet season enhanced soil microbial biomass and altered microbial community structure, resulting in a two-fold increase in net N mineralization rates relative to controls in the early dry season (November). Structural equation modeling showed that the changes in net N mineralization during the early dry season were associated with altered soil microbial communities, dissolved organic N, and litterfall, which were all affected by enhanced soil water content. Our findings suggest that a delayed wet season could have a greater impact on N dynamics than increased precipitation during the wet season. Changes in the seasonal timing of rainfall might therefore influence the functioning of seasonally dry tropical forests.
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Affiliation(s)
- Shiqin Yu
- School of Geography and Remote Sensing, Guangzhou University, Guangzhou 510006, PR China; Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Emma J Sayer
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK; Smithsonian Tropical Research Institute, Balboa, Ancon, Panama City, Panama
| | - Zhian Li
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Qifeng Mo
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, PR China
| | - Mei Wang
- School of Geographic Sciences, South China Normal University, Guangzhou 510631, China
| | - Yingwen Li
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Yongxing Li
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Guoliang Xu
- School of Geography and Remote Sensing, Guangzhou University, Guangzhou 510006, PR China
| | - Zhongmin Hu
- College of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Faming Wang
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China.
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23
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Shen H, Zhang Q, Bi R, Xu X, Zhang X, Fan C, Xiong Z. Linkages of nitrogen-cycling microbial resistance and resilience to soil nutrient stoichiometry under dry-rewetting cycles with different fertilizations and temperatures in a vegetable field. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153294. [PMID: 35066034 DOI: 10.1016/j.scitotenv.2022.153294] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/10/2022] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Multiple dry-rewetting (DRW) cycles occur in intensively managed vegetable fields due to frequent tillage and irrigation. Soil nitrogen (N) cycling depends on the resistance and resilience of related microbial populations to DRW cycles, which could be closely related to soil nutrient status. However, the linkage of N-cycling microbial resistance and resilience and soil nutrient stoichiometry remains unknown in vegetable field. Here, we established four fertilization treatments in a four-year greenhouse vegetable field: no N fertilization, synthesized N fertilization, substituting 50% of chemical N with organic fertilizer or biofertilizer. Then, we set up an 85-day DRW-cycling incubation at 15, 25 and 35 °C including a 55-day fluctuating moisture for microbial resistance and then a 30-day constant moisture for microbial resilience. The results showed that microbial resistance was high (resistance index = 0.87- 0.99) in response to DRW cycles, but microbial resilience was generally low (resilience index = -0.36- 0.76), especially in 50% organic substitution or 15 °C. N-cycling microbes showed an important trade-off between their resistance and resilience to DRW cycles. Furthermore, most treatments showed microbial carbon limitation and N abundance during DRW cycles and recovered gradually to the undisturbed state. Microbial resistance was significantly related to the soil nutrient stoichiometry of carbon, N and phosphorus, while microbial resilience was mainly correlated with carbon-related indicators. In conclusion, N-cycling microbes presented good stability with oligotrophic strategy to frequent DRW cycles, which was linked to not only the historical legacy effect of DRW cycles but also soil nutrient stoichiometry in the vegetable field.
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Affiliation(s)
- Haojie Shen
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qianqian Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; School of Environmental and Resource Sciences, Zhejiang A & F University, Hangzhou 311300, China
| | - Ruiyu Bi
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xintong Xu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi Zhang
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Changhua Fan
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Hainan Key Laboratory of Tropical Eco-circular Agriculture, Danzhou National Agricultural Experimental Station for Agricultural Environment, Institute of Environmental and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zhengqin Xiong
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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24
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Malard LA, Pearce DA. Bacterial Colonisation: From Airborne Dispersal to Integration Within the Soil Community. Front Microbiol 2022; 13:782789. [PMID: 35615521 PMCID: PMC9125085 DOI: 10.3389/fmicb.2022.782789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 04/04/2022] [Indexed: 01/04/2023] Open
Abstract
The deposition of airborne microorganisms into new ecosystems is the first stage of colonisation. However, how and under what circumstances deposited microorganisms might successfully colonise a new environment is still unclear. Using the Arctic snowpack as a model system, we investigated the colonisation potential of snow-derived bacteria deposited onto Arctic soils during and after snowmelt using laboratory-based microcosm experiments to mimic realistic environmental conditions. We tested different melting rate scenarios to evaluate the influence of increased precipitation as well as the influence of soil pH on the composition of bacterial communities and on the colonisation potential. We observed several candidate colonisations in all experiments; with a higher number of potentially successful colonisations in acidoneutral soils, at the average snowmelt rate measured in the Arctic. While the higher melt rate increased the total number of potentially invading bacteria, it did not promote colonisation (snow ASVs identified in the soil across multiple sampling days and still present on the last day). Instead, most potential colonists were not identified by the end of the experiments. On the other hand, soil pH appeared as a determinant factor impacting invasion and subsequent colonisation. In acidic and alkaline soils, bacterial persistence with time was lower than in acidoneutral soils, as was the number of potentially successful colonisations. This study demonstrated the occurrence of potentially successful colonisations of soil by invading bacteria. It suggests that local soil properties might have a greater influence on the colonisation outcome than increased precipitation or ecosystem disturbance.
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Affiliation(s)
- Lucie A. Malard
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, United Kingdom
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- *Correspondence: Lucie A. Malard,
| | - David A. Pearce
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, United Kingdom
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
- David A. Pearce,
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25
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Changes in precipitation patterns can destabilize plant species coexistence via changes in plant-soil feedback. Nat Ecol Evol 2022; 6:546-554. [PMID: 35347257 DOI: 10.1038/s41559-022-01700-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/10/2022] [Indexed: 01/04/2023]
Abstract
Climate change can alter species coexistence through changes in biotic interactions. By describing reciprocal interactions between plants and soil microbes, plant-soil feedback (PSF) has emerged as a powerful framework for predicting plant species coexistence and community dynamics, but little is known about how PSF will respond to changing climate conditions. Hence, the context dependency of PSF has recently gained attention. Water availability is a major driver of all biotic interactions, and it is expected that precipitation patterns will change with ongoing climate change. We tested how soil water content affects PSF by conducting a full factorial pairwise PSF experiment using eight plant species common to southeastern United States coastal prairies under three watering treatments. We found coexistence-stabilizing negative PSF at drier-than-average conditions shifted to coexistence-destabilizing positive PSF under wetter-than-average conditions. A simulation model parameterized with the experimental results supports the prediction that more positive PSF accelerates the erosion of diversity within communities while decreasing the predictability in plant community composition. Our results underline the importance of considering environmental context dependency of PSF in light of a rapidly changing climate.
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26
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Effects of Drought on the Growth of Lespedeza davurica through the Alteration of Soil Microbial Communities and Nutrient Availability. J Fungi (Basel) 2022; 8:jof8040384. [PMID: 35448615 PMCID: PMC9025084 DOI: 10.3390/jof8040384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 01/24/2023] Open
Abstract
Lespedeza davurica (Laxm.) is highly important for reducing soil erosion and maintaining the distinctive natural scenery of semiarid grasslands in northwest China. In this study, a pot experiment was conducted to investigate the effects of drought (20% water-holding capacity) on biomass and its allocation, root characteristics, plant hormones, and soil microbial communities and nutrients after L. davurica was grown in a greenhouse. Drought reduced the total biomass of L. davurica but increased the root:shoot biomass ratio. In addition, drought altered the composition and structure of microbial communities by limiting the mobility of nutrients in non-rhizosphere soils. In particular, drought increased the relative abundances of Basidiomycota, Acidobacteria, Actinobacteria, Coprinellus, Humicola and Rubrobacter, which were closely positively related to the soil organic carbon, pH, available phosphorus, ammonia nitrogen (N) and nitrate N under drought conditions. Furthermore, soil fungi could play a more potentially significant role than that of bacteria in the response of L. davurica to drought. Consequently, our study uncovered the effects of drought on the growth of L. davurica by altering soil microbial communities and/or soil nutrients, thus providing new insights for forage production and natural grassland restoration on the Loess Plateau of China.
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27
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Digestate-Derived Ammonium Fertilizers and Their Blends as Substitutes to Synthetic Nitrogen Fertilizers. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12083787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nutrient recovery from biomass streams generates novel recycling-derived fertilizers (RDFs). The effect of RDFs depends on their nutrient content and variability, which can aid or hinder their use by end-users. Detailed characterization of RDFs can help in evaluating product properties, whereas blending RDFs can optimize their nutrient ratios and reduce nutrient variability. This study assesses ammonium nitrate (AN) from stripping-scrubbing, ammonium water (AW) and concentrate (CaE) from evaporation, and two tailor-made blends (AN + CaE and AW + CaE), for their potential as nitrogen (N) fertilizers in the pot cultivation of lettuce. Parallelly, a soil incubation experiment was conducted to investigate the N release dynamics of the tested RDFs. The RDFs were compared against the commercial calcium ammonium nitrate (CAN) and an unfertilized control. AN and AW fertilization resulted in a similar crop yield and N uptake to the CAN treatment. CaE and blends exhibited poor yield and N uptake, possibly due to the sodium toxicity detected. AN and AW displayed N fertilizer replacement values above 100%, whereas CaE and blends exhibited poor results in the current experiments. The soil incubation experiment showed a positive soil priming effect in AN and AW treatment, as their N release was over 100%. Further research under uncontrolled field conditions utilizing AN and AW for diverse crop types can validate their N replacement potential.
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28
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Guo Z, Bao Y, Liu J. Environmental Difference and Spatial Distance Affect the Fidelity of Variation Source of Microbial Community Structure in Air-Dried Soils. Microorganisms 2022; 10:microorganisms10040672. [PMID: 35456724 PMCID: PMC9031423 DOI: 10.3390/microorganisms10040672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/04/2022] Open
Abstract
Air-dried soil archives are important for microbial ecology research, although the process of air-drying preservation inevitably destroys the original microbial information in soils. Only upon fully understanding the limitations of air-dried soil can it play a greater role. The value of air-dried soil depends on the fidelity of microbial community structure information in the air-dried soil relative to that in fresh soil. To evaluate this, high-throughput sequencing was applied to investigate the microbial community of fresh soils and 227 days air-dried archives from typical farmland under a large spatial scale, and PERMANOVA was used to analyze the explanation proportion (EP) of the spatial factor on the microbial community structure in any paired-fresh or air-dried soils. The results show that for any paired soils, the value of EP ranged from 42.4% to 97.9% (p < 0.001). Importantly, taking fresh soil as a reference, the value of EP declined in air-dried soils (effect size r = 0.79, p < 0.001). Furthermore, the standardized difference in EP between fresh and air-dried soil (NDEP) was used to characterize the fidelity of variance source of microbial community structure in air-dried soils, and correlation tests showed that NDEP was negatively correlated with spatial distance (r = −0.21, p < 0.01) and with environmental difference (r = −0.37, p < 0.001). Further analyses show that larger NDEP was observed at a spatial distance <25 km or an environmental difference <0.58. Variance partitioning analysis showed that 28.0% of the variation in NDEP could be explained, with environmental difference constituting 14.0% and the interaction between the environmental difference and spatial distance constituting the remaining 14.0%. Soil texture was the most important factor for predicting NDEP, followed by soil pH and annual average temperature. This study not only emphasizes the possible decline in EP when using air-dried soils to reveal microbial community patterns, but also implies that air-dried soil is more suitable for addressing scientific questions under a large spatial scale or environmental differences.
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Affiliation(s)
- Zhiying Guo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.B.); (J.L.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
| | - Yuanyuan Bao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.B.); (J.L.)
| | - Jie Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.B.); (J.L.)
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29
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Almeida BK, Cline E, Sklar F, Afkhami ME. Hydrology shapes microbial communities and microbiome‐mediated growth of an Everglades tree island species. Restor Ecol 2022. [DOI: 10.1111/rec.13677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brianna K. Almeida
- Department of Biology University of Miami Coral Gables Florida 33146 USA
| | - Eric Cline
- South Florida Water Management District West Palm Beach Florida 33406 USA
| | - Fred Sklar
- South Florida Water Management District West Palm Beach Florida 33406 USA
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30
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Evans S, Allison S, Hawkes C. Microbes, memory, and moisture: predicting microbial moisture responses and their impact on carbon cycling. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sarah Evans
- W.K. Kellogg Biological Station, Ecology and Evolutionary Biology Program Department of Integrative Biology Michigan State University Hickory Corners MI 49083 USA
| | - Steve Allison
- Department of Ecology and Evolutionary Biology Department of Earth System Science University of California Irvine California 92697 USA
| | - Christine Hawkes
- Department of Plant and Microbial Biology North Carolina State University Raleigh NC 27607 USA
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31
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Wang T, Duan Y, Liu G, Shang X, Liu L, Zhang K, Li J, Zou Z, Zhu X, Fang W. Tea plantation intercropping green manure enhances soil functional microbial abundance and multifunctionality resistance to drying-rewetting cycles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:151282. [PMID: 34757096 DOI: 10.1016/j.scitotenv.2021.151282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/11/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Climate change leads to more serious drying-rewetting alternation disturbance, which furtherly affects soil ecosystem function and agriculture production. Intercropping green manure, as an ancient agricultural practice, can improve the physical, chemical, and biological fertility of soil in tea plantation. However, the effects of intercropping green manure on soil multifunctional resistance to drying-rewetting disturbance in tea plantation has not been reported. In this study, the effects of different green manure practices over four years (tea plant monoculture, tea plant and soybean intercropping, tea plant and soybean + milk vetch intercropping) on soil multifunctionality resistance to drying-rewetting cycles, and the pivotal influencing factors were investigated. We used quantitative PCR array and analysis of multiple enzyme activities to characterize the abundance of functional genes and ecosystem multifunctionality, respectively. Compared with tea plantation monoculture, tea plant intercropping soybean and soybean + milk vetch significantly increased multifunctionality resistance by 12.07% and 25.86%, respectively. Random forest analysis indicated that rather than the diversity, the abundance of functional genes was the major drive of multifunctionality resistance. The structure equation model further proved that tea plantation intercropping green manure could improve the abundance of C cycling related functional genes mediated by soil properties, and ultimately increased multifunctionality resistance to drying-rewetting disturbance. Therefore, tea plantation intercropping green manure is an effective approach to maintain the multifunctionality resistance, which is conducive to maintain the soil nutrient supply capacity and tea production under the disturbance of drying-rewetting alternation.
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Affiliation(s)
- Ting Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Duan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guodong Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaowen Shang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lefeng Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kexin Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinqiu Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongwei Zou
- Department of Plant Science, University of Manitoba, Winnipeg R3T2N2, Canada
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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32
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Ji RQ, Xie ML, Li GL, Xu Y, Gao TT, Xing PJ, Meng LP, Liu SY. Response of bacterial community structure to different ecological niches and their functions in Korean pine forests. PeerJ 2022; 10:e12978. [PMID: 35251783 PMCID: PMC8893031 DOI: 10.7717/peerj.12978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 01/31/2022] [Indexed: 01/11/2023] Open
Abstract
A healthy plant microbiome is diverse, taxonomically-structured, and gives its plant host moderate advantages in growth, development, stress tolerance, and disease resistance. The plant microbiome varies with ecological niches and is influenced by variables that are complex and difficult to separate from each other, such as the plant species, soil, and environmental factors. To explore the composition, diversity, and functions of the bacterial community of Korean pine forests, we used high-throughput sequencing to study five areas with different forest ages from June to October 2017 in northeast China. We obtained 3,247 operational taxonomic units (OTUs) based on 16S rRNA gene sequencing via an Illumina Hi-seq platform. A total of 36 phyla and 159 known genera were classified. The Shannon index of the bacterial community from the rhizospheric soil was significantly higher (p < 0.01, n = 10) than that of the root tips. Beta-diversity analysis confirmed that the bacterial community of the rhizospheric soil was significantly different (p < 0.001) from the root tips. Nine bacterial phyla were dominant (relative richness > 1%) in the rhizospheric soil, but there were six dominant phyla in the root tips. Proteobacteria was the core flora in the root tips with a relative abundance of more than 50%. It is known that the formation of bacterial communities in the rhizospheric soil or the root is mainly caused by the processes of selection, and we found a relatively high abundance of a few dominant species. We further analyzed the correlations between the bacterial community from the rhizospheric soil with that of the root tips, as well as the correlations of the bacterial community with soil physicochemical properties and climate factors. We used Functional Annotation of the Prokaryotic Tax (FAPROTAX) to predict the functions of the bacterial community in the rhizospheric soil and root tips. Five related phototrophic functions, nine nitrogen cycle functions, two related chemoheterotrophic functions, and two others were predicted. The abundance of the bacteria phyla performing relevant functions was different in the rhizospheric soil than in the root tips. These functions were significantly influenced by the contents of nitrogen, phosphorus, and potassium in the soil habitat. The bacterial composition and functions in the rhizospheric soil and root tips of Korean pine were analyzed, and the results demonstrated the importance of soil and plant species on the bacterial community in the below ground plant microbiome.
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Affiliation(s)
- Rui-Qing Ji
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China,Key Laboratory of Edible Fungus Resources Utilization in North China, Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, Jilin Province, China
| | - Meng-Le Xie
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China,Life Science College, Northeast Normal University, Changchun, Jilin Province, China
| | - Guan-Lin Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China
| | - Yang Xu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China
| | - Ting-Ting Gao
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China
| | - Peng-Jie Xing
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China
| | - Li-Peng Meng
- Wood Research Institute, Jilin Forestry Science Institute, Changchun, Jilin Province, China
| | - Shu-Yan Liu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China
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33
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Bi W, Weng B, Yan D, Wang H, Wang M, Yan S, Jing L, Liu T, Chang W. Responses of Phosphate-Solubilizing Microorganisms Mediated Phosphorus Cycling to Drought-Flood Abrupt Alternation in Summer Maize Field Soil. Front Microbiol 2022; 12:768921. [PMID: 35111138 PMCID: PMC8802831 DOI: 10.3389/fmicb.2021.768921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
Soil microbial communities are essential to phosphorus (P) cycling, especially in the process of insoluble phosphorus solubilization for plant P uptake. Phosphate-solubilizing microorganisms (PSM) are the dominant driving forces. The PSM mediated soil P cycling is easily affected by water condition changes due to extreme hydrological events. Previous studies basically focused on the effects of droughts, floods, or drying-rewetting on P cycling, while few focused on drought-flood abrupt alternation (DFAA), especially through microbial activities. This study explored the DFAA effects on P cycling mediated by PSM and P metabolism-related genes in summer maize field soil. Field control experiments were conducted to simulate two levels of DFAA (light drought-moderate flood, moderate drought-moderate flood) during two summer maize growing periods (seeding-jointing stage, tasseling-grain filling stage). Results showed that the relative abundance of phosphate-solubilizing bacteria (PSB) and phosphate-solubilizing fungi (PSF) increased after DFAA compared to the control system (CS), and PSF has lower resistance but higher resilience to DFAA than PSB. Significant differences can be found on the genera Pseudomonas, Arthrobacter, and Penicillium, and the P metabolism-related gene K21195 under DFAA. The DFAA also led to unstable and dispersed structure of the farmland ecosystem network related to P cycling, with persistent influences until the mature stage of summer maize. This study provides references for understanding the micro process on P cycling under DFAA in topsoil, which could further guide the DFAA regulations.
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Affiliation(s)
- Wuxia Bi
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Baisha Weng
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- Yinshanbeilu Grassland Eco-Hydrology National Observation and Research Station, China Institute of Water Resources and Hydropower Research, Beijing, China
- *Correspondence: Baisha Weng, ,
| | - Denghua Yan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- Yinshanbeilu Grassland Eco-Hydrology National Observation and Research Station, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Hao Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Mengke Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Siying Yan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- College of Resource Environment and Tourism, Capital Normal University, Beijing, China
| | - Lanshu Jing
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Tiejun Liu
- Yinshanbeilu Grassland Eco-Hydrology National Observation and Research Station, China Institute of Water Resources and Hydropower Research, Beijing, China
- Collaborative Innovation Center for Grassland Ecological Security (Jointly Supported by the Ministry of Education of China and Inner Mongolia Autonomous Region), Hohhot, China
| | - Wenjuan Chang
- College of Hydraulic and Environmental Engineering, China Three Gorges University, Yichang, China
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Dacal M, García‐Palacios P, Asensio S, Wang J, Singh BK, Maestre FT. Climate change legacies contrastingly affect the resistance and resilience of soil microbial communities and multifunctionality to extreme drought. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14000] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Marina Dacal
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramon Margalef’ Universidad de Alicante San Vicente del Raspeig Spain
- Departamento de Biología y Geología Física y Química Inorgánica Universidad Rey Juan Carlos Móstoles Spain
| | - Pablo García‐Palacios
- Departamento de Biología y Geología Física y Química Inorgánica Universidad Rey Juan Carlos Móstoles Spain
- Instituto de Ciencias Agrarias Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Sergio Asensio
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramon Margalef’ Universidad de Alicante San Vicente del Raspeig Spain
| | - Juntao Wang
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
- Global Centre for Land‐Based Innovation Western Sydney University Penrith South DC NSW Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
- Global Centre for Land‐Based Innovation Western Sydney University Penrith South DC NSW Australia
| | - Fernando T. Maestre
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramon Margalef’ Universidad de Alicante San Vicente del Raspeig Spain
- Departamento de Ecología Universidad de Alicante San Vicente del Raspeig Spain
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Eppinga MB, Van der Putten WH, Bever JD. Plant-soil feedback as a driver of spatial structure in ecosystems. Phys Life Rev 2022; 40:6-14. [DOI: 10.1016/j.plrev.2022.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/17/2022] [Indexed: 12/16/2022]
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Metabolic flexibility of aerobic methanotrophs under anoxic conditions in Arctic lake sediments. THE ISME JOURNAL 2022; 16:78-90. [PMID: 34244610 PMCID: PMC8692461 DOI: 10.1038/s41396-021-01049-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023]
Abstract
Methane (CH4) emissions from Arctic lakes are a large and growing source of greenhouse gas to the atmosphere with critical implications for global climate. Because Arctic lakes are ice covered for much of the year, understanding the metabolic flexibility of methanotrophs under anoxic conditions would aid in characterizing the mechanisms responsible for limiting CH4 emissions from high-latitude regions. Using sediments from an active CH4 seep in Lake Qalluuraq, Alaska, we conducted DNA-based stable isotope probing (SIP) in anoxic mesocosms and found that aerobic Gammaproteobacterial methanotrophs dominated in assimilating CH4. Aerobic methanotrophs were also detected down to 70 cm deep in sediments at the seep site, where anoxic conditions persist. Metagenomic analyses of the heavy DNA from 13CH4-SIP incubations showed that these aerobic methanotrophs had the capacity to generate intermediates such as methanol, formaldehyde, and formate from CH4 oxidation and to oxidize formaldehyde in the tetrahydromethanopterin (H4MPT)-dependent pathway under anoxic conditions. The high levels of Fe present in sediments, combined with Fe and CH4 profiles in the persistent CH4 seep site, suggested that oxidation of CH4, or, more specifically, its intermediates such as methanol and formaldehyde might be coupled to iron reduction. Aerobic methanotrophs also possessed genes associated with nitrogen and hydrogen metabolism, which might provide potentially alternative energy conservation options under anoxic conditions. These results expand the known metabolic spectrum of aerobic methanotrophs under anoxic conditions and necessitate the re-assessment of the mechanisms underlying CH4 oxidation in the Arctic, especially under lakes that experience extended O2 limitations during ice cover.
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Hall NC, Sikaroodi M, Hogan D, Jones RC, Gillevet PM. The Presence of Denitrifiers In Bacterial Communities of Urban Stormwater Best Management Practices (BMPs). ENVIRONMENTAL MANAGEMENT 2022; 69:89-110. [PMID: 34860281 PMCID: PMC8758610 DOI: 10.1007/s00267-021-01529-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Stormwater best management practices (BMPs) are engineered structures that attempt to mitigate the impacts of stormwater, which can include nitrogen inputs from the surrounding drainage area. The goal of this study was to assess bacterial community composition in different types of stormwater BMP soils to establish whether a particular BMP type harbors more denitrification potential. Soil sampling took place over the summer of 2015 following precipitation events. Soils were sampled from four bioretention facilities, four dry ponds, four surface sand filters, and one dry swale. 16S rRNA gene analysis of extracted DNA and RNA amplicons indicated high bacterial diversity in the soils of all BMP types sampled. An abundance of denitrifiers was also indicated in the extracted DNA using presence/absence of nirS, nirK, and nosZ denitrification genes. BMP soil bacterial communities were impacted by the surrounding soil physiochemistry. Based on the identification of a metabolically-active community of denitrifiers, this study has indicated that denitrification could potentially occur under appropriate conditions in all types of BMP sampled, including surface sand filters that are often viewed as providing low potential for denitrification. The carbon content of incoming stormwater could be providing bacterial communities with denitrification conditions. The findings of this study are especially relevant for land managers in watersheds with legacy nitrogen from former agricultural land use.
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Affiliation(s)
- Natalie C Hall
- U.S. Geological Survey, Florence Bascom Geoscience Center, Reston, VA, USA.
| | - Masoumeh Sikaroodi
- Department of Biology, George Mason University, Manassas, VA, USA
- Microbiome Analysis Center (MBAC), Manassas, VA, USA
| | - Dianna Hogan
- U.S. Geological Survey, Deputy Regional Director for Science, Southeast Region, Reston, VA, USA
| | - R Christian Jones
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
- Potomac Environmental Research and Education Center (PEREC), George Mason University, Woodbridge, VA, USA
| | - Patrick M Gillevet
- Department of Biology, George Mason University, Manassas, VA, USA
- Microbiome Analysis Center (MBAC), Manassas, VA, USA
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Mahood AL, Jones RO, Board DI, Balch JK, Chambers JC. Interannual climate variability mediates changes in carbon and nitrogen pools caused by annual grass invasion in a semiarid shrubland. GLOBAL CHANGE BIOLOGY 2022; 28:267-284. [PMID: 34614268 PMCID: PMC9291498 DOI: 10.1111/gcb.15921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/26/2021] [Indexed: 05/13/2023]
Abstract
Exotic plant invasions alter ecosystem properties and threaten ecosystem functions globally. Interannual climate variability (ICV) influences both plant community composition (PCC) and soil properties, and interactions between ICV and PCC may influence nitrogen (N) and carbon (C) pools. We asked how ICV and non-native annual grass invasion covary to influence soil and plant N and C in a semiarid shrubland undergoing widespread ecosystem transformation due to invasions and altered fire regimes. We sampled four progressive stages of annual grass invasion at 20 sites across a large (25,000 km2 ) landscape for plant community composition, plant tissue N and C, and soil total N and C in 2013 and 2016, which followed 2 years of dry and wet conditions, respectively. Multivariate analyses and ANOVAs showed that in invasion stages where native shrub and perennial grass and forb communities were replaced by annual grass-dominated communities, the ecosystem lost more soil N and C in wet years. Path analysis showed that high water availability led to higher herbaceous cover in all invasion stages. In stages with native shrubs and perennial grasses, higher perennial grass cover was associated with increased soil C and N, while in annual-dominated stages, higher annual grass cover was associated with losses of soil C and N. Also, soil total C and C:N ratios were more homogeneous in annual-dominated invasion stages as indicated by within-site standard deviations. Loss of native shrubs and perennial grasses and forbs coupled with annual grass invasion may lead to long-term declines in soil N and C and hamper restoration efforts. Restoration strategies that use innovative techniques and novel species to address increasing temperatures and ICV and emphasize maintaining plant community structure-shrubs, grasses, and forbs-will allow sagebrush ecosystems to maintain C sequestration, soil fertility, and soil heterogeneity.
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Affiliation(s)
- Adam L. Mahood
- Department of GeographyUniversity of Colorado BoulderBoulderColoradoUSA
- Earth LabUniversity of ColoradoBoulderColoradoUSA
| | - Rachel O. Jones
- Department of Biological & Ecological EngineeringOregon State UniversityCorvallisOregonUSA
| | - David I. Board
- US Forest ServiceRocky Mountain Research StationRenoNevadaUSA
| | - Jennifer K. Balch
- Department of GeographyUniversity of Colorado BoulderBoulderColoradoUSA
- Earth LabUniversity of ColoradoBoulderColoradoUSA
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Fikri M, Joulian C, Motelica-Heino M, Norini MP, Hellal J. Resistance and Resilience of Soil Nitrogen Cycling to Drought and Heat Stress in Rehabilitated Urban Soils. Front Microbiol 2021; 12:727468. [PMID: 35002993 PMCID: PMC8727462 DOI: 10.3389/fmicb.2021.727468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/12/2021] [Indexed: 11/21/2022] Open
Abstract
In the context of climate change and biodiversity loss, rehabilitation of degraded urban soils is a means of limiting artificialization of terrestrial ecosystems and preventing further degradation of soils. Ecological rehabilitation approaches are available to reinitiate soil functions and enhance plant development. However, little is known about the long-term stability of rehabilitated soils in terms of soil functions when further natural or anthropogenic perturbations occur. Based on rehabilitated urban soils, the present study sought to evaluate the resistance and resilience of soil functions linked to carbon cycling and phosphate dynamics in addition to nitrogen cycling and related microbial communities after a heat and drought stress. A laboratory experiment was conducted in microcosms under controlled temperature conditions, with four contrasted soils collected from a rehabilitated urban brownfield; an initial, non-rehabilitated soil (IS), a technosol with a high organic matter level (HO), and two technosols with less organic matter (LO1 and LO2), together with their respective controls (no stress). Changes in potential denitrification (PDR), nitrification (PNR) rates, and their interactive relationships with soil microbial activities and soil physicochemical properties were determined following a combined heat (40°C) and drought stress period of 21 days. Measurements were carried out immediately after the stress (resistance), and then also 5, 30, and 92 days after soil rewetting at 60% water holding capacity (resilience). Microbial activities involved in soil functions such as carbon cycling and phosphate dynamics proved to be of low resistance in all soils except for IS; however, they were resilient and recovered rapidly after rewetting. On the other hand, the microbial activities and gene abundances that were measured in relation to nitrogen cycling processes showed that for denitrification, activities were more rapidly resilient than gene abundances whereas for nitrification the activities and gene abundances were resilient in the same way. Results suggest that, unless the soils contain high amounts of organic matter, microbial communities in imported soils can be more vulnerable to environmental pressures such as drought and heat than communities already present. This should be considered when rehabilitating degraded soils.
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Affiliation(s)
- Mehdi Fikri
- BRGM, DEPA/GME, Orléans, France
- ISTO, UMR 7327, CNRS-Université d’Orléans-Brgm, Orléans, France
| | | | | | | | - Jennifer Hellal
- BRGM, DEPA/GME, Orléans, France
- *Correspondence: Jennifer Hellal,
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Sengupta A, Volkmann THM, Danczak RE, Stegen JC, Dontsova K, Abramson N, Bugaj AS, Volk MJ, Matos KA, Meira-Neto AA, Barberán A, Neilson JW, Maier RM, Chorover J, Troch PA, Meredith LK. Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System. Front Microbiol 2021; 12:754698. [PMID: 34887842 PMCID: PMC8650109 DOI: 10.3389/fmicb.2021.754698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.
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Affiliation(s)
- Aditi Sengupta
- Department of Biology, California Lutheran University, Thousand Oaks, CA, United States.,Biosphere 2, University of Arizona, Tucson, AZ, United States
| | | | - Robert E Danczak
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - James C Stegen
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Katerina Dontsova
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Nate Abramson
- Department of Geosciences, University of Arizona, Tucson, AZ, United States
| | - Aaron S Bugaj
- Biosphere 2, University of Arizona, Tucson, AZ, United States
| | - Michael J Volk
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | | | - Antonio A Meira-Neto
- Department of Hydrology and Atmospheric Sciences, University of Arizona, Tucson, AZ, United States
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Julia W Neilson
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Raina M Maier
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Jon Chorover
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Peter A Troch
- Department of Hydrology and Atmospheric Sciences, University of Arizona, Tucson, AZ, United States
| | - Laura K Meredith
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
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Ma W, Yang Z, Liang L, Ma Q, Wang G, Zhao T. Seasonal Changes in Soil Microbial Community and Co-Occurrence Network of Species of the Genus Corylus. Microorganisms 2021; 9:microorganisms9112228. [PMID: 34835354 PMCID: PMC8625130 DOI: 10.3390/microorganisms9112228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 11/21/2022] Open
Abstract
Hazelnut is one of the four major nuts in the world and has high nutritional and economic value. This study employed Illumina sequencing of ITS rDNA and 16S rRNA genes to identify the seasonal changes in soil microbial community, the predominant environmental factors driving microbial community composition, and the differences in soil microbial composition among different species of the genus Corylus. We found that the soil microbial community composition of species of Corylus changed significantly with the change in seasons. Corylus heterophylla and Corylus kweichowensis had more ectomycorrhiza in their soil compared to Corylus avellane. The main factor influencing fungal community composition in soil was the available potassium, while that of bacteria was the total phosphorus content. Co-occurrence network analysis revealed that the ratio of positive interaction to negative interaction in soil of C. heterophylla and Ping’ou (C. heterophylla × C. avellane) was higher, while the negative interaction of soil community structure in C. avellane was greater. The bacterial community was more stable than the fungal community according to microbial diversity and co-occurrence network analyses. The findings of this research may facilitate improvements to the production and soil system management in hazel planting processes.
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Affiliation(s)
- Wenxu Ma
- State Key Laboratory of Tree Genetics and Breeding, Beijing 100091, China; (W.M.); (Z.Y.); (L.L.); (Q.M.); (G.W.)
- Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing 100091, China
| | - Zhen Yang
- State Key Laboratory of Tree Genetics and Breeding, Beijing 100091, China; (W.M.); (Z.Y.); (L.L.); (Q.M.); (G.W.)
- Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing 100091, China
| | - Lisong Liang
- State Key Laboratory of Tree Genetics and Breeding, Beijing 100091, China; (W.M.); (Z.Y.); (L.L.); (Q.M.); (G.W.)
- Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing 100091, China
| | - Qinghua Ma
- State Key Laboratory of Tree Genetics and Breeding, Beijing 100091, China; (W.M.); (Z.Y.); (L.L.); (Q.M.); (G.W.)
- Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing 100091, China
| | - Guixi Wang
- State Key Laboratory of Tree Genetics and Breeding, Beijing 100091, China; (W.M.); (Z.Y.); (L.L.); (Q.M.); (G.W.)
- Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing 100091, China
| | - Tiantian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Beijing 100091, China; (W.M.); (Z.Y.); (L.L.); (Q.M.); (G.W.)
- Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Forestry and Grassland Innovation Alliance on Hazelnut, Beijing 100091, China
- Correspondence: ; Tel.: +86-010-62888537
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Huang Y, Ren W, Liu H, Wang H, Xu Y, Han Y, Teng Y. Contrasting impacts of drying-rewetting cycles on the dissipation of di-(2-ethylhexyl) phthalate in two typical agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148433. [PMID: 34146807 DOI: 10.1016/j.scitotenv.2021.148433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 06/12/2023]
Abstract
Di-(2-ethylhexyl) phthalate (DEHP) pollution has become a growing problem in farmlands of China. Drying-rewetting (DW) cycle is one of frequent environmental changes that agricultural production is confronted with, and also a convenient and practical agronomic regulation measure. In this study, in order to explore the effects of DW cycles on the dissipation of DEHP and their driving mechanisms in different types of soils, we performed a 45-day microcosm culture experiment with two typical agricultural soils, Lou soil (LS) and Red soil (RS). High-throughput sequencing was applied to study the response of soil microbial communities in the process of DEHP dissipation under DW cycles. The results showed that the DW cycles considerably inhibited the dissipation of DEHP in LS while promoted that in RS. The DW cycles obviously decreased the diversity, the relative abundance of significantly differential bacteria, and the total abundance of potential degrading bacterial groups in LS, whereas have little effect on bacterial community in RS, except at the initial cultivation stage when the corresponding parameters were promoted. The inhibition of the DW cycles on DEHP dissipation in LS was mainly derived from microbial degradation, but the interplay between microbial functions and soil attributes contributed to the promotion of DEHP dissipation in RS under the DW cycles. This comprehensive understanding of the contrasting impacts and underlying driving mechanisms may provide crucial implications for the prevention and control of DEHP pollution in regional soils.
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Affiliation(s)
- Yiwen Huang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; School of Environment and Safety Engineering, Changzhou University, Changzhou 213164, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Haoran Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Huimin Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujuan Han
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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Duan Y, Chen R, Zhang R, Jiang W, Chen X, Yin C, Mao Z. Isolation, Identification, and Antibacterial Mechanisms of Bacillus amyloliquefaciens QSB-6 and Its Effect on Plant Roots. Front Microbiol 2021; 12:746799. [PMID: 34603274 PMCID: PMC8482014 DOI: 10.3389/fmicb.2021.746799] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/26/2021] [Indexed: 01/22/2023] Open
Abstract
Apple replant disease (ARD) is a common problem in major apple planting areas, and biological factors play a leading role in its etiology. Here, we isolated the bacterial strain QSB-6 from the rhizosphere soil of healthy apple trees in a replanted orchard using the serial dilution method. Strain QSB-6 was provisionally identified as Bacillus amyloliquefaciens based on its morphology, physiological and biochemical characteristics, carbon source utilization, and chemical sensitivity. Maximum likelihood analysis based on four gene sequences [16S ribosomal RNA gene (16S rDNA), DNA gyrase subunit A (gyrA), DNA gyrase subunit B (gyrB), and RNA polymerase subunit B (rpoB)] from QSB-6 and other strains indicated that it had 100% homology with B. amyloliquefaciens, thereby confirming its identification. Flat standoff tests showed that strain QSB-6 had a strong inhibitory effect on Fusarium proliferatum, Fusarium solani, Fusarium verticillioides, Fusarium oxysporum, Alternaria alternata, Aspergillus flavus, Phoma sp., Valsa mali, Rhizoctonia solani, Penicillium brasilianum, and Albifimbria verrucaria, and it had broad-spectrum antibacterial characteristics. Extracellular metabolites from strain QSB-6 showed a strong inhibitory effect on Fusarium hyphal growth and spore germination, causing irregular swelling, atrophy, rupture, and cytoplasmic leakage of fungal hyphae. Analysis of its metabolites showed that 1,2-benzenedicarboxylic acid and benzeneacetic acid, 3- hydroxy-, methyl ester had good inhibitory effects on Fusarium, and increased the length of primary roots and the number of lateral roots of Arabidopsis thaliana plantlet. Pot experiments demonstrated that a QSB-6 bacterial fertilizer treatment (T2) significantly improved the growth of Malus hupehensis Rehd. seedlings. It increased root length, surface area, tips, and forks, respiration rate, protective enzyme activities, and the number of soil bacteria while reducing the number of soil fungi. Fermentation broth from strain QSB-6 effectively prevented root damage from Fusarium. terminal restriction fragment length polymorphism (T-RFLP) and quantitative PCR (qPCR) assays showed that the T2 treatment significantly reduced the abundance of Fusarium in the soil and altered the soil fungal community structure. In summary, B. amyloliquefaciens QSB-6 has a good inhibitory effect on Fusarium in the soil and can significantly promote plant root growth. It has great potential as a biological control agent against ARD.
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Affiliation(s)
- Yanan Duan
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, China
| | - Ran Chen
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, China
| | - Rong Zhang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, China
| | - Weitao Jiang
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, China
| | - Xuesen Chen
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, China
| | - Chengmiao Yin
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, China
| | - Zhiquan Mao
- National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, China
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Macrofungi Cultivation in Shady Forest Areas Significantly Increases Microbiome Diversity, Abundance and Functional Capacity in Soil Furrows. J Fungi (Basel) 2021; 7:jof7090775. [PMID: 34575813 PMCID: PMC8469386 DOI: 10.3390/jof7090775] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/10/2021] [Accepted: 09/10/2021] [Indexed: 12/18/2022] Open
Abstract
Cultivating macrofungi is an important management measure to develop economy in shady forest areas; however, its effect on soil ecology, especially microbial abundance and structure, remains insufficiently studied. Herein, in a subtropical forestland, soil chemical and enzyme analyses, metagenomic sequencing and quantitative real-time PCR were employed to evaluate the impact of Stropharia rugosoannulata cultivation on soil microbiomes in three niches: soil below fungal beds, soil from furrows, and control forest soil with no influence from mushroom cultivation. Nutrients were accumulated in the soil below fungal beds with a significant increase (p < 0.05) in SOC, total C, total N, available P, and the activities of glucosidase and cellobiosidase. Non-metric multidimensional scaling and PERMANOVA results indicated that the structure of the microbiomes had been significantly (p < 0.05) shaped among the different niches. Soil furrows were microbial hotspots characterized by the higher microbial diversity and richness. Moreover, the increased microbiome abundance (assessed through qPCR) and the high number of significant stimulated functional types (based on MetaCyc genome database) indicated an enhanced functional capacity in furrows. Together, these results provide a comprehensive understanding of the microbial assemblies and the differently influenced soil properties in mushroom cultivation areas.
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Liu P, Chen S, Cui Y, Tan W. Insights into the inhibition effects of Cd on soil enzyme activities: From spatial microscale to macroscale. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126274. [PMID: 34102356 DOI: 10.1016/j.jhazmat.2021.126274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
Cd is a heavy metal with high toxicity and adverse influence on the activities of soil enzymes. However, how Cd toxicity varies with the microenvironment or different regions needs further investigation. In this study, 17 soil samples were collected from different locations in China. Each soil sample was divided into two parts in accordance with aggregate size, macroaggregate fraction (> 250 µm) and microaggregate fraction (< 250 µm). The inhibitory effects of Cd on three soil enzymes were analyzed. Results showed that on the microscale, the inhibitory effect of Cd in macroaggregates was significantly stronger than that in microaggregates. Moreover, the inhibitory effect of Cd varied obviously across different regions, with the greatest effects being observed in soils from northeast China. This result indicates that the temperature and precipitation played a synergistic role in the Cd inhibition effects. The Cd inhibition ratios showed significantly negative correlations with clay content and positive correlations with pH value and organic carbon content, indicating that soil clay, pH and organic carbon were the main factors determining the Cd inhibition ratios on enzyme activities. This suggests that factors on the microscale and macroscale should be considered in addressing Cd pollution in soils.
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Affiliation(s)
- Ping Liu
- Technical Centre for Soil, Agriculture and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing 100012, China
| | - Sheng Chen
- Technical Centre for Soil, Agriculture and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing 100012, China
| | - Yini Cui
- State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Wenbing Tan
- State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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Sünnemann M, Alt C, Kostin JE, Lochner A, Reitz T, Siebert J, Schädler M, Eisenhauer N. Low‐intensity land‐use enhances soil microbial activity, biomass and fungal‐to‐bacterial ratio in current and future climates. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marie Sünnemann
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Institute of Biology Leipzig University Leipzig Germany
| | - Christina Alt
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Faculty of Biology Technical University Dresden Dresden Germany
| | - Julia E. Kostin
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Faculty of Management Science and Economics Leipzig University Leipzig Germany
| | - Alfred Lochner
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Institute of Biology Leipzig University Leipzig Germany
| | - Thomas Reitz
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Soil Ecology Helmholtz‐Centre for Environmental Research – UFZ Halle Germany
| | - Julia Siebert
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Institute of Biology Leipzig University Leipzig Germany
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Community Ecology Helmholtz‐Centre for Environmental Research – UFZ Halle Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Institute of Biology Leipzig University Leipzig Germany
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47
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Mu Z, Dong S, Li Y, Li S, Shen H, Zhang J, Han Y, Xu Y, Zhao Z. Soil Bacterial Community Responses to N Application and Warming in a Qinghai-Tibetan Plateau Alpine Steppe. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.709518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nitrogen deposition and climate warming can alter soil bacterial communities. However, the response of soil bacteria in an alpine steppe to these changes is largely unknown. In this study, a field experiment was performed on the northeastern Qinghai-Tibetan Plateau to determine the changes in soil bacterial communities of alpine steppes in response to nitrogen application and warming. The experiment consisted of four treatments, namely no-N application with no-warming (CK), N application (8 kg N ha−1 year−1) with no-warming (N), warming with no-N application (W), and N application (8 kg N ha−1 year−1) with warming (W&N). This study aimed to investigate (1) the changes in soil bacterial diversity and community structure under simulated nitrogen deposition and warming conditions, and (2) the key environmental factors responsible for these changes. Based on the results, soil bacterial diversity and community composition did not change significantly in the short term. Warming had a significant effect on overall bacterial composition, rare species composition, and individual bacterial taxa. Besides, the interaction between nitrogen application and warming had a significant effect on community β-diversity. Above-ground plant variables were highly correlated with bacterial community characteristics. Nitrogen application and warming did not significantly alter the distribution range of the bacterial community. Overall, this study suggests that soil bacterial communities can remain relatively stable at the level of simulated nitrogen application and warming and that short-term climatic changes may have no significant impacts on soil bacterial communities.
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48
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Mod HK, Buri A, Yashiro E, Guex N, Malard L, Pinto-Figueroa E, Pagni M, Niculita-Hirzel H, van der Meer JR, Guisan A. Predicting spatial patterns of soil bacteria under current and future environmental conditions. THE ISME JOURNAL 2021; 15:2547-2560. [PMID: 33712699 PMCID: PMC8397778 DOI: 10.1038/s41396-021-00947-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 02/01/2023]
Abstract
Soil bacteria are largely missing from future biodiversity assessments hindering comprehensive forecasts of ecosystem changes. Soil bacterial communities are expected to be more strongly driven by pH and less by other edaphic and climatic factors. Thus, alkalinisation or acidification along with climate change may influence soil bacteria, with subsequent influences for example on nutrient cycling and vegetation. Future forecasts of soil bacteria are therefore needed. We applied species distribution modelling (SDM) to quantify the roles of environmental factors in governing spatial abundance distribution of soil bacterial OTUs and to predict how future changes in these factors may change bacterial communities in a temperate mountain area. Models indicated that factors related to soil (especially pH), climate and/or topography explain and predict part of the abundance distribution of most OTUs. This supports the expectations that microorganisms have specific environmental requirements (i.e., niches/envelopes) and that they should accordingly respond to environmental changes. Our predictions indicate a stronger role of pH over other predictors (e.g. climate) in governing distributions of bacteria, yet the predicted future changes in bacteria communities are smaller than their current variation across space. The extent of bacterial community change predictions varies as a function of elevation, but in general, deviations from neutral soil pH are expected to decrease abundances and diversity of bacteria. Our findings highlight the need to account for edaphic changes, along with climate changes, in future forecasts of soil bacteria.
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Affiliation(s)
- Heidi K Mod
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland.
| | - Aline Buri
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Erika Yashiro
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lucie Malard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Marco Pagni
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hélène Niculita-Hirzel
- Department of Occupational Health and Environment, Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | | | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
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Borsodi AK, Mucsi M, Krett G, Szabó A, Felföldi T, Szili-Kovács T. Variation in Sodic Soil Bacterial Communities Associated with Different Alkali Vegetation Types. Microorganisms 2021; 9:microorganisms9081673. [PMID: 34442752 PMCID: PMC8402138 DOI: 10.3390/microorganisms9081673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/15/2021] [Accepted: 08/04/2021] [Indexed: 11/22/2022] Open
Abstract
In this study, we examined the effect of salinity and alkalinity on the metabolic potential and taxonomic composition of microbiota inhabiting the sodic soils in different plant communities. The soil samples were collected in the Pannonian steppe (Hungary, Central Europe) under extreme dry and wet weather conditions. The metabolic profiles of microorganisms were analyzed using the MicroResp method, the bacterial diversity was assessed by cultivation and next-generation amplicon sequencing based on the 16S rRNA gene. Catabolic profiles of microbial communities varied primarily according to the alkali vegetation types. Most members of the strain collection were identified as plant associated and halophilic/alkaliphilic species of Micrococcus, Nesterenkonia, Nocardiopsis, Streptomyces (Actinobacteria) and Bacillus, Paenibacillus (Firmicutes) genera. Based on the pyrosequencing data, the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes and Bacteroidetes also changed mainly with the sample types, indicating distinctions within the compositions of bacterial communities according to the sodic soil alkalinity-salinity gradient. The effect of weather extremes was the most pronounced in the relative abundance of the phyla Actinobacteria and Acidobacteria. The type of alkali vegetation caused greater shifts in both the diversity and activity of sodic soil microbial communities than the extreme aridity and moisture.
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Affiliation(s)
- Andrea K. Borsodi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. Sétány 1/C, H-1117 Budapest, Hungary; (M.M.); (G.K.); (T.F.)
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, H-1113 Budapest, Hungary;
- Correspondence: (A.K.B.); (T.S.-K.); Tel.: +36-13812177 (A.K.B.); +36-309617452 (T.S.-K.)
| | - Márton Mucsi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. Sétány 1/C, H-1117 Budapest, Hungary; (M.M.); (G.K.); (T.F.)
- Institute for Soil Sciences, Centre for Agricultural Research, Herman Ottó út 15, H-1022 Budapest, Hungary
| | - Gergely Krett
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. Sétány 1/C, H-1117 Budapest, Hungary; (M.M.); (G.K.); (T.F.)
| | - Attila Szabó
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, H-1113 Budapest, Hungary;
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. Sétány 1/C, H-1117 Budapest, Hungary; (M.M.); (G.K.); (T.F.)
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, H-1113 Budapest, Hungary;
| | - Tibor Szili-Kovács
- Institute for Soil Sciences, Centre for Agricultural Research, Herman Ottó út 15, H-1022 Budapest, Hungary
- Correspondence: (A.K.B.); (T.S.-K.); Tel.: +36-13812177 (A.K.B.); +36-309617452 (T.S.-K.)
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50
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Susanti WI, Bartels T, Krashevska V, Widyastuti R, Deharveng L, Scheu S, Potapov A. Conversion of rainforest into oil palm and rubber plantations affects the functional composition of litter and soil Collembola. Ecol Evol 2021; 11:10686-10708. [PMID: 34367606 PMCID: PMC8328430 DOI: 10.1002/ece3.7881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/10/2021] [Accepted: 06/18/2021] [Indexed: 11/10/2022] Open
Abstract
Rainforest conversion and expansion of plantations in tropical regions are associated with changes in animal communities and biodiversity decline. In soil, Collembola are one of the most numerous invertebrate groups that affect the functioning of microbial communities and support arthropod predators. Despite that, information on the impact of changes in land use in the tropics on species and trait composition of Collembola communities is very limited. We investigated the response of Collembola to the conversion of rainforest into rubber agroforestry ("jungle rubber"), rubber, and oil palm plantations in Jambi Province (Sumatra, Indonesia), a region which experienced one of the strongest recent deforestation globally. Collembola were sampled in 2013 and 2016 from the litter and soil layer using heat extraction, and environmental factors were measured (litter C/N ratio, pH, water content, composition of microbial community and predator abundance). In the litter layer, density and species richness in plantation systems were 25%-38% and 30%-40% lower, respectively, than in rainforest. However, in the soil layer, density, species richness, and trait diversity of Collembola were only slightly affected by land-use change, contrasting the response of many other animal groups. Species and trait composition of Collembola communities in litter and soil differed between each of the land-use systems. Water content and pH were identified as main factors related to the differences in species and trait composition in both litter and soil, followed by the density of micro- and macropredators. Dominant species of Collembola in rainforest and jungle rubber were characterized by small body size, absence of furca, and absence of intense pigmentation, while in plantations, larger species with long furca and diffuse or patterned pigmentation were more abundant. Overall, land-use change negatively affected Collembola communities in the litter layer, but its impact was lower in the soil layer. Several pantropical genera of Collembola (i.e., Isotomiella, Pseudosinella, and Folsomides) dominated across land-use systems, reflecting their high environmental adaptability and/or efficient dispersal, calling for studies on their ecology and genetic diversity. The decline in species richness and density of litter-dwelling Collembola with the conversion of rainforest into plantation systems calls for management practices mitigating negative effects of the deterioration of the litter layer in rubber plantations, but even more in oil palm plantations.
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Affiliation(s)
- Winda Ika Susanti
- J.F. Blumenbach Institute of Zoology and AnthropologyUniversity of GöttingenGoettingenGermany
- Department of Soil Sciences and Land ResourcesInstitut Pertanian Bogor (IPB)BogorIndonesia
| | - Tamara Bartels
- J.F. Blumenbach Institute of Zoology and AnthropologyUniversity of GöttingenGoettingenGermany
| | - Valentyna Krashevska
- J.F. Blumenbach Institute of Zoology and AnthropologyUniversity of GöttingenGoettingenGermany
| | - Rahayu Widyastuti
- Department of Soil Sciences and Land ResourcesInstitut Pertanian Bogor (IPB)BogorIndonesia
| | - Louis Deharveng
- UMR7205CNRSMuséum national d'Histoire naturelleInstitut de Systématique, Évolution, Biodiversité (ISYEB)Sorbonne UniversitéParisFrance
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and AnthropologyUniversity of GöttingenGoettingenGermany
- Centre of Biodiversity and Sustainable Land UseGöttingenGermany
| | - Anton Potapov
- J.F. Blumenbach Institute of Zoology and AnthropologyUniversity of GöttingenGoettingenGermany
- Russian Academy of SciencesA.N. Severtsov Institute of Ecology and EvolutionMoscowRussia
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