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Gupta VVSR, Tiedje JM. Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales. MLIFE 2024; 3:21-41. [PMID: 38827504 PMCID: PMC11139212 DOI: 10.1002/mlf2.12116] [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: 09/27/2023] [Revised: 01/05/2024] [Accepted: 02/05/2024] [Indexed: 06/04/2024]
Abstract
The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat-based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro-organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.
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Affiliation(s)
| | - James M. Tiedje
- Centre for Microbial EcologyMichigan State UniversityEast LansingMichiganUSA
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Sun D, Huang Y, Wang Z, Tang X, Ye W, Cao H, Shen H. Soil microbial community structure, function and network along a mangrove forest restoration chronosequence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169704. [PMID: 38163592 DOI: 10.1016/j.scitotenv.2023.169704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/23/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
Mangrove forests have high ecological, social and economic values, but due to environmental changes and human activities, natural mangrove forests have experienced serious degradations and reductions in distribution area worldwide. In the coastal zones of southern China, an introduced mangrove species, Sonneratia apetala, has been extensively used for mangrove restoration because of its rapid growth and strong environmental adaptability. However, little is known about how soil microorganisms vary with the restoration stages of the afforested mangrove forests. Here, we examined the changes in soil physicochemical properties and microbial biomass, community structure and function, and network in three afforested S. apetala forests with restoration time of 7, 12, and 18 years and compared them with a bare flat and a 60-year-old natural Kandelia obovata forest in a mangrove nature reserve. Our results showed that the contents of soil salinity, organic carbon, total nitrogen, ammonium nitrogen, and microbial biomass increased, while soil pH and bacterial alpha diversity decreased with afforestation age. Soil microbial community structure was significantly affected by soil salinity, organic carbon, pH, total nitrogen, ammonium nitrogen, available phosphorus, and available kalium, and susceptibility to environmental factors was more pronounced in bacterial than fungal community structure. The relative abundances of aerobic chemoheterotrophy were significantly higher in 12- and 18-year-old S. apetala than in K. obovata forest, while that of sulfate-reducing bacteria showed a decreasing trend with afforestation age. The abundance of dung saprotroph was significantly higher in 12- and 18-year-old S. apetala forests than in the natural forest. With the increasing afforestation age, the modularity of microbial networks increased, while stability and robustness decreased. Our results suggest that planting S. apetala contributes to improving soil fertility and microbial biomass but may make soil microbial networks more vulnerable.
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Affiliation(s)
- Dangge Sun
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiyi Huang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhangming Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuli Tang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanhui Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Honglin Cao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Shen
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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Ren Z, Ye S, Li H, Huang X, Chen L, Cao S, Chen T. Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau. MICROBIAL ECOLOGY 2023; 86:2756-2769. [PMID: 37542537 DOI: 10.1007/s00248-023-02280-0] [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: 03/26/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023]
Abstract
Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.
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Affiliation(s)
- Ze Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 Beijing East Road, Nanjing, 210008, China.
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, 519087, China.
| | - Shudan Ye
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Hongxuan Li
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Xilei Huang
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Luyao Chen
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Shengkui Cao
- School of Geographical Science, Qinghai Normal University, Xining, 810008, China
| | - Tao Chen
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, 768 Jiayuguan W Road, Lanzhou, 730020, China.
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Luo X, Gong Y, Xu F, Wang S, Tao Y, Yang M. Soil horizons regulate bacterial community structure and functions in Dabie Mountain of the East China. Sci Rep 2023; 13:15866. [PMID: 37739984 PMCID: PMC10517015 DOI: 10.1038/s41598-023-42981-7] [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: 11/01/2022] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
Soil bacterial communities regulate nutrient cycling and plant growth in forests. Although these bacterial communities vary with soil nutrients and plant traits, the variation and degree with soil horizons in different forest types remain unclear. Here, bacterial communities of 44 soil samples from organic horizon (O horizon) and mineral horizon (M horizon) of three forest types (Cunninghamia, broad-leaved and Pinus forests) in subtropical forests of Dabie Mountain, China were analyzed based on amplicon sequencing. We assessed the effects of soil horizons and forest types on bacterial communities. The results showed that the bacterial richness and diversity were significantly higher in the O horizon than in the M horizon. Furthermore, the bacterial community composition and functions were also remarkably different between the two soil horizons. Furthermore, forest types could affect bacterial community composition but not for diversity and functions. Moreover, soil organic matter, including the total organic carbon, available phosphorus, total organic nitrogen, available potassium, ammonium nitrogen, and pH were main drivers for bacterial community composition. The results propose robust evidence that soil horizons strongly driven bacterial community composition and diversity, and suggest that microhabitat of soil bacterial communities is important to maintain the stability of forest ecosystem.
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Affiliation(s)
- Xia Luo
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China.
| | - Yinping Gong
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
| | - Feiyan Xu
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
| | - Shuai Wang
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
| | - Yingying Tao
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
| | - Mengmeng Yang
- School of Biological Science and Food Engineering, Chuzhou University, No. 1 Huifeng West Road, Chuzhou, 239000, Anhui, China
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Sui X, Li M, Frey B, Dai G, Yang L, Li MH. Effect of elevation on composition and diversity of fungi in the rhizosphere of a population of Deyeuxia angustifolia on Changbai Mountain, northeastern China. Front Microbiol 2023; 14:1087475. [PMID: 37266006 PMCID: PMC10231489 DOI: 10.3389/fmicb.2023.1087475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/27/2023] [Indexed: 06/03/2023] Open
Abstract
Soil fungi are a key component of terrestrial ecosystems and play a major role in soil biogeochemical cycling. Although the diversity and composition of fungal communities are regulated by many abiotic and biotic factors, the effect of elevation on soil fungal community diversity and composition remains largely unknown. In this study, the soil fungal composition and diversity in Deyeuxia angustifolia populations along an elevational gradient (1,690 m to 2020 m a.s.l.) were assessed, using Illumina MiSeq sequencing, on the north-facing slope of the Changbai Mountain, northeastern China. Our results showed that soil physicochemical parameters changed significantly along with the elevational gradients. The Ascomycota and Basidiomycota were the most dominant phyla along with the gradient. Alpha diversity of soil fungi decreased significantly with elevation. Soil nitrate nitrogen (NO3--N) was positively correlated with fungal richness and phylogenetic diversity (PD), indicating that soil nitrate nitrogen (NO3--N) is a key soil property determining fungal community diversity. In addition to soil nitrate content, soil pH and soil moisture were the most important environmental properties determining the soil fungal diversity. Our results suggest that the elevational changes in soil physicochemical properties play a key role in shaping the community composition and diversity of soil fungi. This study will allow us to better understand the biodiversity distribution patterns of soil microorganisms in mountain ecosystems.
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Affiliation(s)
- Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Mengsha Li
- School of Forestry, Northeast Forestry University, Harbin, China
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Beat Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Guanhua Dai
- Research Station of Changbai Mountain Forest Ecosystems, Chinese Academy of Sciences, Erdaobaihe, China
| | - Libin Yang
- School of Forestry, Northeast Forestry University, Harbin, China
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Mai-He Li
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
- School of Life Sciences, Hebei University, Baoding, China
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Ren Z, Ma K, Jia X, Wang Q, Zhang C, Li X. Metagenomics Unveils Microbial Diversity and Their Biogeochemical Roles in Water and Sediment of Thermokarst Lakes in the Yellow River Source Area. MICROBIAL ECOLOGY 2023; 85:904-915. [PMID: 35650293 DOI: 10.1007/s00248-022-02053-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/25/2022] [Indexed: 05/04/2023]
Abstract
Thermokarst lakes have long been recognized as biogeochemical hotspots, especially as sources of greenhouse gases. On the Qinghai-Tibet Plateau, thermokarst lakes are experiencing extensive changes due to faster warming. For a deep understanding of internal lake biogeochemical processes, we applied metagenomic analyses to investigate the microbial diversity and their biogeochemical roles in sediment and water of thermokarst lakes in the Yellow River Source Area (YRSA). Sediment microbial communities (SMCs) had lower species and gene richness than water microbial communities (WMCs). Bacteria were the most abundant component in both SMCs and WMCs with significantly different abundant genera. The functional analyses showed that both SMCs and WMCs had low potential in methanogenesis but strong in aerobic respiration, nitrogen assimilation, exopolyphosphatase, glycerophosphodiester phosphodiesterases, and polyphosphate kinase. Moreover, SMCs were enriched in genes involved in anaerobic carbon fixation, aerobic carbon fixation, fermentation, most nitrogen metabolism pathways, dissimilatory sulfate reduction, sulfide oxidation, polysulfide reduction, 2-phosphonopropionate transporter, and phosphate regulation. WMCs were enriched in genes involved in assimilatory sulfate reduction, sulfur mineralization, phosphonoacetate hydrolase, and phosphonate transport. Functional potentials suggest the differences of greenhouse gas emission, nutrient cycling, and living strategies between SMCs and WMCs. This study provides insight into the main biogeochemical processes and their properties in thermokarst lakes in YRSA, improving our understanding of the roles and fates of these lakes in a warming world.
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Affiliation(s)
- Ze Ren
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China.
- School of Environment, Beijing Normal University, Beijing, 100875, China.
| | - Kang Ma
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Xuan Jia
- College of Education for the Future, Beijing Normal University, Zhuhai, 519087, China
| | - Qing Wang
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Cheng Zhang
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Engineering Technology, Beijing Normal University, Zhuhai, 519087, China
| | - Xia Li
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Environment, Beijing Normal University, Beijing, 100875, China
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Stanek M, Kushwaha P, Murawska-Wlodarczyk K, Stefanowicz AM, Babst-Kostecka A. Quercus rubra invasion of temperate deciduous forest stands alters the structure and functions of the soil microbiome. GEODERMA 2023; 430:116328. [PMID: 37600960 PMCID: PMC10438910 DOI: 10.1016/j.geoderma.2023.116328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Invasive plants can modify the diversity and taxonomical structure of soil microbiomes. However, it is difficult to generalize the underlying factors as their influence often seems to depend on the complex plant-soil-microbial interactions. In this paper, we investigated how Quercus rubra impacts on the soil microbiome across two soil horizons in relation to native woodland. Five paired adjacent invaded vs native vegetation plots in a managed forest in southern Poland were investigated. Soil microbial communities were assessed along with soil enzyme activities and soil physicochemical parameters, separately for both organic and mineral horizons, as well as forest stand characteristics to explore plant-soil-microbe interactions. Although Q. rubra did not significantly affect pH, organic C, total N, available nutrients nor enzymatic activity, differences in soil abiotic properties (except C to N ratio) were primarily driven by soil depth for both vegetation types. Further, we found significant differences in soil microbiome under invasion in relation to native vegetation. Microbial richness and diversity were lower in both horizons of Q. rubra vs control plots. Moreover, Q. rubra increased relative abundance of unique amplicon sequence variants in both horizons and thereby significantly changed the structure of the core soil microbial communities, in comparison to the control plots. In addition, predicted microbial functional groups indicated a predominant soil depth effect in both vegetation plots with higher abundance of aerobic chemoheterotrophic bacteria and endophytic fungi in the organic horizon and greater abundance of methanotrophic and methylotrophic bacteria, and ectomycorrhizal fungi in the mineral horizon. Overall, our results indicate strong associations between Q. rubra invasion and changes in soil microbiome and associated functions, a finding that needs to be further investigated to predict modifications in ecosystem functioning caused by this invasive species.
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Affiliation(s)
- Małgorzata Stanek
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Priyanka Kushwaha
- Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
| | | | - Anna M. Stefanowicz
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Alicja Babst-Kostecka
- Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
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Li B, Liu X, Zhu D, Su H, Guo K, Sun G, Li X, Sun L. Crop diversity promotes the recovery of fungal communities in saline-alkali areas of the Western Songnen Plain. Front Microbiol 2023; 14:1091117. [PMID: 36819047 PMCID: PMC9930164 DOI: 10.3389/fmicb.2023.1091117] [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: 11/06/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
Introduction Phytoremediation is an effective strategy for saline land restoration. In the Western Songnen Plain, northeast China, soil fungal community recovery for saline phytoremediation has not been well documented among different cropping patterns. In this study, we tested how rotation, mixture, and monoculture cropping patterns impact fungal communities in saline-alkali soils to assess the variability between cropping patterns. Methods The fungal communities of the soils of the different cropping types were determined using Illumina Miseq sequencing. Results Mixture and rotation promoted an increase in operational taxonomic unit (OTU) richness, and OTU richness in the mixture system decreased with increasing soil depth. A principal coordinate analysis (PCoA) showed that cropping patterns and soil depths influenced the structure of fungal communities, which may be due to the impact of soil chemistry. This was reflected by soil total nitrogen (TN) and electrical conductivity (EC) being the key factors driving OTU richness, while soil available potassium (AK) and total phosphorus (TP) were significantly correlated with the relative abundance of fungal dominant genus. The relative abundance of Leptosphaerulina, Alternaria, Myrothecium, Gibberella, and Tetracladium varied significantly between cropping patterns, and Leptosphaerulina was significantly associated with soil chemistry. Soil depth caused significant differences in the relative abundance of Fusarium in rotation and mixture soils, with Fusarium more commonly active at 0-15 cm deep soil. Null-model analysis revealed that the fungal community assembly of the mixture soils in 0-15 cm deep soil was dominated by deterministic processes, unlike the other two cropping patterns. Furthermore, fungal symbiotic networks were more complex in rotation and mixture than in monoculture soils, reflected in more nodes, more module hubs, and connectors. The fungal networks in rotation and mixture soils were more stable than in monoculture soils, and mixture networks were obviously more connected than rotations. FUNGuild showed that the relative proportion of saprotroph in rotation and mixture was significantly higher than that in monocultures. The highest proportion of pathotroph and symbiotroph was exhibited in rotation and mixture soils, respectively. Discussion Overall, mixture is superior to crop rotation and monocultures in restoring fungal communities of the saline-alkali soils of the Western Songnen Plain, northeast China.
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Affiliation(s)
- Bin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Xiaoqian Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Dan Zhu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Heng Su
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Kaiwen Guo
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Guangyu Sun
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Xin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China,School of Forestry, Northeast Forestry University, Harbin, China,*Correspondence: Xin Li, ✉
| | - Lei Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, China,Lei Sun, ✉
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Lyu D, Smith DL. The root signals in rhizospheric inter-organismal communications. FRONTIERS IN PLANT SCIENCE 2022; 13:1064058. [PMID: 36618624 PMCID: PMC9811129 DOI: 10.3389/fpls.2022.1064058] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Root exudates play a key role in mediating plant-plant and plant-rhizomicrobiome interactions, including regulating biochemical/physiological aspects of plant-associated microorganisms, to enhance host plant growth and resilience. Root exudates can act as signals to reduce the competition from neighboring plants and recruiting/choreographing a wide range of diverse rhizomicrobiome members to make the host plant a good fit with its immediate environment. Root exudate production is a dynamic and key process, but there is a limited understanding of the metabolites or metabolic pathways involved in the inter-organismal communications facilitated by them. Given the well-known symbiotic relationships between plants and associated rhizomicrobiome members, adding root exudates to microbial isolation media may allow some of the large segments of rhizomicrobiome members that are not currently culturable to be grown in vitro. This will provide new insights into how root signals orchestrate associated microbes, will benefit agricultural production in the face of challenges posed by climate change, and will help to sustainably provide food for a growing global human population.
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Li W, Xie L, Zhao C, Hu X, Yin C. Nitrogen Fertilization Increases Soil Microbial Biomass and Alters Microbial Composition Especially Under Low Soil Water Availability. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02103-8. [PMID: 36044056 DOI: 10.1007/s00248-022-02103-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Soil microbial biomass and composition are affected by resource supply and water availability. However, the response of soil microbial communities to nitrogen fertilization under different water availability conditions is unclear. Therefore, this study conducted a 6-year pot experiment comprising five watering regimes (40%, 50%, 60%, 80%, and 100% of field capacity (FC)) and three nitrogen fertilization levels (NH4NO3 solution; 0 [N0], 20 [N1], and 40 [N2] g N m-2 year-1) to investigate soil microbial biomass, composition, and properties. The results indicated that soil microbial biomass and composition were more strongly affected by nitrogen fertilization compared with water regime. Nitrogen fertilization increased soil microbial biomass and altered soil microbial community composition, especially under low soil water availability. Soil microbial biomass was positively linearly associated with soil water regimes under N0, whereas it responded polynomially to soil water regimes under N1 and N2. The maximal soil microbial biomass was observed at FC80 for N1 and FC60 for N2. Furthermore, the biomass of soil microbial groups with high nitrogen and carbon acquisition ability as well as the enzyme activities of carbon and nitrogen cycling (β-1,4-glucosidase and β-1,4-N-acetyl-glucosaminidase, respectively) were stimulated by nitrogen fertilization. Soil microbial biomass was affected directly by nitrogen fertilization and indirectly by nitrogen and water regimes, via altering soil pH, dissolved inorganic nitrogen (NH4+-N and NO3--N) concentration, and soil organic carbon concentration. This study provides new insights into the effect of interaction between soil nitrogen and water availabilities on soil microbial biomass, composition, and its underlying mechanism.
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Affiliation(s)
- Wanting Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Lulu Xie
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Chunzhang Zhao
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, People's Republic of China
| | - Xuefeng Hu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, People's Republic of China
| | - Chunying Yin
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, 610041, People's Republic of China.
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Ren Z, Gao H. Abundant and rare soil fungi exhibit distinct succession patterns in the forefield of Dongkemadi glacier on the central Qinghai-Tibet Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154563. [PMID: 35302033 DOI: 10.1016/j.scitotenv.2022.154563] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Glaciers are retreating rapidly, exposing extensive new soil habitats in glacier forefields and providing unique areas for studying primary succession. However, understanding the variation patterns and assembly mechanisms of abundant and rare fungi subcommunities along the glacier-retreating chronosequence remains a knowledge gap, especially true for the vast Qinghai-Tibet Plateau (QTP). Here, we investigated fungal communities in the glacier forefield in Dongkemadi Glaicer on the central QTP. The results showed that fungal alpha diversity exhibited a clear increasing pattern in response to increasing of distance to glacier. The percentage of abundant OTUs decreased while the percentage of rare OTUs increased, suggesting that soil development is more beneficial to the rare taxa. The distributions of both abundant and rare subcommunities exhibited a clear spatial pattern along the distance to glacier, and might be strongly controlled by multiple environmental variables, including pH, soil moisture, vegetation status, soil organic carbon, total nitrogen, and soluble reactive phosphorus. Abundant and rare fungal subcommunities were structured in different assembly regimes. Dispersal limitation processes were dominant for both abundant and rare subcommunities but with a stronger contribution to abundant subcommunity assembly. Heterogeneous selection processes contributed higher and non-dominant processes contributed lower to abundant subcommunities than to rare subcommunities. The modular structure of the fungal co-occurrence network was highly localized along the soil chronosequence. By revealing distinct diversity patterns and community assembly mechanisms of abundant and rare fungal subcommunities, our study improved our understanding of ecological succession along the glacier-retreating chronosequence.
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Affiliation(s)
- Ze Ren
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai 519087, China; School of Environment, Beijing Normal University, Beijing 100875, China
| | - Hongkai Gao
- Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China.
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Ren Z, Zhang Y, Li X, Zhang C. Biogeography of Micro-Eukaryotic Communities in Sediment of Thermokarst Lakes Are Jointly Controlled by Spatial, Climatic, and Physicochemical Factors Across the Qinghai-Tibet Plateau. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.901107] [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
Thermokarst lakes are formed following ice-rich permafrost thaw and widely distribute in the cold regions with high latitude and elevation. However, the micro-eukaryotic communities (MECs) in thermokarst lakes are not well studied. Employing 18S rRNA gene sequencing, we assessed the biogeography of MECs and their driving factors in sediments of thermokarst lakes across the Qinghai-Tibet Plateau (QTP). Results showed that Diatom, Gastrotricha, Nematozoa, Ciliophora, and Cercozoa were dominant lineages in relative abundance and OTU richness. MECs varied substantially across the lakes in terms of diversity and composition. Structural equation modeling and mantel test showed that both OTU richness and community structure of MECs had close relationships with spatial factors, climatic factors, and sediment properties, particularly with latitude, mean annual precipitation, pH, as well as nutrient concentrations and stoichiometric ratios. Moreover, different groups of microbial eukaryotes (taxonomic groups and co-occurrence modules) responded differentially to the measured environmental variables. The results suggested that the biogeography of sediment MECs of thermokarst lakes on the QTP were jointly controlled by spatial and climatic factors as well as sediment properties. This study provides the first view of the composition, diversity, and underlying drivers of MECs dynamic in surface sediments of thermokarst lakes across the QTP.
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