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Li Q, Cheng X, Liu X, Gao P, Wang H, Su C, Huang Q. Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts. Front Microbiol 2024; 15:1377721. [PMID: 38659982 PMCID: PMC11041041 DOI: 10.3389/fmicb.2024.1377721] [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: 01/28/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl- played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.
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Affiliation(s)
- Qing Li
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xiaoyan Liu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Pengfei Gao
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- School of Environmental Studies, China University of Geosciences, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Chuntian Su
- Institute of Karst Geology, CAGS/Key Laboratory of Karst Dynamics, MNR & GZAR, Guilin, China
- Pingguo Guangxi, Karst Ecosystem, National Observation and Research Station, Pingguo, Guangxi, China
| | - Qibo Huang
- Institute of Karst Geology, CAGS/Key Laboratory of Karst Dynamics, MNR & GZAR, Guilin, China
- Pingguo Guangxi, Karst Ecosystem, National Observation and Research Station, Pingguo, Guangxi, China
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2
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Nayak PK, Nayak AK, Panda BB, Senapati A, Panneerselvam P, Kumar A, Tripathi R, Poonam A, Shahid M, Mohapatra SD, Kaviraj M, Kumar U. Rice-based integrated farming system improves the soil quality, bacterial community structure and system productivity under sub-humid tropical condition. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:65. [PMID: 38321197 DOI: 10.1007/s10653-024-01863-1] [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: 08/23/2023] [Accepted: 01/07/2024] [Indexed: 02/08/2024]
Abstract
Rice-based integrated farming system improves the productivity and profitability by recycling resources efficiently. In the sub-humid tropics, rice production without sufficient nutrient replenishment often leads to soil health and fertility degradation. There has been very limited research on soil health and fertility after adopting a multi-enterprising rice-based integrated farming system (IFS), notably in the rice-fish-livestock and agroforestry system, when compared to a conventional farming system (CS). Therefore, the present study analyzed the dynamics of soil properties, soil bacterial community structure and their possible interaction mechanisms, as well as their effect on regulating soil quality and production in IFS, IFSw (water stagnant area of IFS) and CS. The results indicated that soil nutrient dynamics, bacterial diversity indices (Shannon index, Simpson index, Chao 1, ACE and Fisher index) and system productivity were higher in IFSw and IFS compared to CS. Moreover, relative operational taxonomic units of dominant bacterial genera (Chloroflexi, Acidobacteria, Verrucomicrobia, Planctomycetes, Cyanobacteria, Crenarchaeota and Gemmatimonadetes) were also higher in IFSw and IFS compared to CS. Mean soil quality index (SQI) was highest in IFSw (0.780 ± 0.201) followed by IFS (0.770 ± 0.080) and CS (0.595 ± 0.244). Moreover, rice equivalent yields (REY) and rice yields were well correlated with the higher levels of soil biological indices (SQIBiol) in IFS. Overall, our results revealed that rice-based IFS improved the soil health and fertility and ensuing crop productivity through positive interaction with soil bacterial communities and nutrient stoichiometry leading to agroecosystem sustainability.
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Affiliation(s)
| | - A K Nayak
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - B B Panda
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - A Senapati
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - P Panneerselvam
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - A Kumar
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - R Tripathi
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - A Poonam
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - M Shahid
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - S D Mohapatra
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Megha Kaviraj
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Upendra Kumar
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India.
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Hussain S, Chen M, Liu Y, Mustafa G, Wang X, Liu J, Sheikh TMM, Bano H, Yasoob TB. Composition and assembly mechanisms of prokaryotic communities in wetlands, and their relationships with different vegetation and reclamation methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:166190. [PMID: 37567310 DOI: 10.1016/j.scitotenv.2023.166190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/26/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Coastal wetlands are undergoing substantial transformations globally as a result of increased human activities. However, compared to other ecosystems, diversity and functional characteristics of microbial communities in reclaimed coastal wetlands are not well studied compared to other ecosystems. This is important because it is known that microorganisms can play a crucial role in biogeochemical cycling within coastal wetland ecosystems. Hence, this study utilized the high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in reclaimed coastal wetlands. The results revealed a substantial change in soil properties following coastal wetland reclamation. Remarkably, the reclaimed soil exhibited significantly lower pH, soil organic carbon (SOC), and total salinity (TS) values (p < 0.05). The dominant phyla included Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Planctomycetes among study sites. However, the relative abundance of Proteobacteria increased from un-reclaimed coastal wetlands to reclaimed ones. The Proteobacteria, Chloroflexi, and Acidobacteria showed higher relative abundance in vegetated soil compared to bare soil, while Bacteroidetes and Planctomycetes exhibited the opposite trend. Notably, vegetation types exerted the strongest influence on microbial diversity, surpassing the effects of soil types and depth (F = 34.49, p < 0.001; F = 25.49, p < 0.001; F = 3.173, p < 0.078, respectively). Stochastic assembly processes dominated in un-reclaimed soil, whereas deterministic processes governed the assembly in artificial sea embankment wetlands (SEW). The presence of Spartina alterniflora in all soil types (except SEW soils) indicated stochastic assembly, while Phragmites australis in reclaimed soils pointed toward deterministic microbial assembly. Furthermore, environmental factors such as pH, soil water content (SWC), SOC, total carbon (TC), total nitrogen (TN), total phosphorus (TP), NH4+-N, vegetation types, soil depth, and geographic distance exhibited significant effects on microbial beta diversity indices. Co-occurrence network analysis revealed a stronger association between taxa in SEW compared to land reclaimed from wetlands (LRW) and natural coastal wetlands (NCW). The bottom soil layer exhibited more complex network interactions than the topsoil layer. Besides soil parameters, reclamation and varieties of vegetation were also substantial factors influencing the composition, diversity, and assembly processes of microbial communities in coastal wetlands.
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Affiliation(s)
- Sarfraz Hussain
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Min Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Yuhong Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Ghulam Mustafa
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Xue Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Jiayuan Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Taha Majid Mahmood Sheikh
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; Institute of Plant Protection, Jiangsu Academy of Agriculture Sciences, Nanjing, China
| | - Hamida Bano
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; Department of animal sciences, Faculty of agricultural Sciences, Ghazi university, Dera Ghazi Khan, Pakistan
| | - Talat Bilal Yasoob
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China; Department of Zoology, University of Education, Lahore, Pakistan
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Pinheiro Alves de Souza Y, Schloter M, Weisser W, Schulz S. Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum. MICROBIAL ECOLOGY 2023; 86:2882-2893. [PMID: 37624441 PMCID: PMC10640511 DOI: 10.1007/s00248-023-02285-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023]
Abstract
Despite its enormous importance for ecosystem services, factors driving microbial recolonization of soils after disturbance are still poorly understood. Here, we compared the microbial recolonization patterns of a disturbed, autoclaved soil using different amounts of the original non-disturbed soil as inoculum. By using this approach, we manipulated microbial biomass, but did not change microbial diversity of the inoculum. We followed the development of a new soil microbiome after reinoculation over a period of 4 weeks using a molecular barcoding approach as well as qPCR. Focus was given on the assessment of bacteria and archaea. We could show that 1 week after inoculation in all inoculated treatments bacterial biomass exceeded the values from the original soil as a consequence of high dissolved organic carbon (DOC) concentrations in the disturbed soil resulting from the disturbance. This high biomass was persistent over the complete experimental period. In line with the high DOC concentrations, in the first 2 weeks of incubation, copiotrophic bacteria dominated the community, which derived from the inoculum used. Only in the disturbed control soils which did not receive a microbial inoculum, recolonization pattern differed. In contrast, archaeal biomass did not recover over the experimental period and recolonization was strongly triggered by amount of inoculated original soil added. Interestingly, the variability between replicates of the same inoculation density decreased with increasing biomass in the inoculum, indicating a deterministic development of soil microbiomes if higher numbers of cells are used for reinoculation.
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Affiliation(s)
- Yuri Pinheiro Alves de Souza
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Neuherberg, Germany
- Technische Universität München, TUM School of Life Science, Chair of Environmental Microbiology, Freising, Germany
| | - Michael Schloter
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Neuherberg, Germany
- Technische Universität München, TUM School of Life Science, Chair of Environmental Microbiology, Freising, Germany
| | - Wolfgang Weisser
- Technische Universität München, TUM School of Life Science, Chair of Terrestrial Ecology, Freising, Germany
| | - Stefanie Schulz
- Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Neuherberg, Germany.
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Chen Q, Li D, Luo N, Yang J. Differences in Juniperus przewalskii Rhizosphere Microbiomes across Age Classes: Community Diversity and Assembly. Microorganisms 2023; 11:2094. [PMID: 37630654 PMCID: PMC10458523 DOI: 10.3390/microorganisms11082094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Evidence shows that biotic and abiotic factors have apparent diversity at different forest ages, leading to changes in rhizosphere microbiomes. However, the difference in diversity, co-occurrence pattern, and assembly of the rhizosphere microbial community among the different forest ages is still unclear. A total of 24 Juniperus przewalskii rhizosphere soil samples were selected from four representative age classes, using diameter at breast height (DBH) as a proxy for tree age (age class I: 5 < DBH ≤ 12.5 cm, age class II: 12.5 < DBH ≤ 22.5 cm, age class III: 22.5 < DBH ≤ 32.5 cm, and age class IV: DBH > 32.5 cm), and analyzed the structural characteristics of the soil microbial community by high-throughput amplicon sequencing. With the increase in age class, the microbial community α-diversity and β-diversity had an increased trend. The bacterial Shannon index in class II and class III were markedly higher than in class I. From class I to class IV, the relative abundances of dominant phyla such as Actinobacteria and Ascomycota decreased, and the relative abundances of Proteobacteria and Basidiomycota increased in contrast. The complexity and association stability of the bacteria and fungi community network structure increase with forest age. Stochastic processes mediated the assembly of soil bacterial communities, while deterministic processes played a more significant role in the assembly of fungal communities. In addition, the relative importance of deterministic components in the microbial community increased significantly with age class. Random forests suggested that soil pH, plant Shannon-Wiener index (H), and Pielou's evenness index (J) were the most important driving factors of bacterial and fungal community assembly. Overall, these results provide information useful for understanding the generation and maintenance mechanisms of rhizosphere microbial communities across age classes.
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Affiliation(s)
| | - Dengwu Li
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (Q.C.); (N.L.); (J.Y.)
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Ma M, Zhao Y, Jiang X, Guan D, Yuan M, Cao F, Li L, Zhou J, Ding J, Li J. Fertilization altered co-occurrence patterns and microbial assembly process of ammonia-oxidizing microorganisms. Sci Rep 2023; 13:8234. [PMID: 37217543 DOI: 10.1038/s41598-022-26293-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/13/2022] [Indexed: 05/24/2023] Open
Abstract
Ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) are important intermediate links in the nitrogen cycle. Apart from the AOA and AOB communities in soil, we further investigated co-occurrence patterns and microbial assembly processes subjected to inorganic and organic fertilizer treatments for over 35 years. The amoA copy numbers and AOA and AOB communities were found to be similar for the CK and organic fertilizer treatments. Inorganic fertilizers decreased the AOA gene copy numbers by 0.75-0.93-fold and increased the AOB gene copy numbers by 1.89-3.32-fold compared to those of the CK treatment. The inorganic fertilizer increased Nitrososphaera and Nitrosospira. The predominant bacteria in organic fertilizer was Nitrosomonadales. Furthermore, the inorganic fertilizer increased the complexity of the co-occurrence pattern of AOA and decreased the complexity pattern of AOB comparing with organic fertilizer. Different fertilizer had an insignificant effect on the microbial assembly process of AOA. However, great difference exists in the AOB community assembly process: deterministic process dominated in organic fertilizer treatment and stochastic processes dominated in inorganic fertilizer treatment, respectively. Redundancy analysis indicated that the soil pH, NO3-N, and available phosphorus contents were the main factors affecting the changes in the AOA and AOB communities. Overall, this findings expanded our knowledge concerning AOA and AOB, and ammonia-oxidizing microorganisms were more disturbed by inorganic fertilizers than organic fertilizers.
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Affiliation(s)
- Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Yubin Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China.
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Ming Yuan
- Qiqihar Sub-Academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, 161006, Heilongjiang, China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Li Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Jing Zhou
- School of Life Sciences, Qufu Normal University, Jining, 273165, China
| | - Jianli Ding
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China.
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Wahdan SFM, Ji L, Schädler M, Wu YT, Sansupa C, Tanunchai B, Buscot F, Purahong W. Future climate conditions accelerate wheat straw decomposition alongside altered microbial community composition, assembly patterns, and interaction networks. THE ISME JOURNAL 2023; 17:238-251. [PMID: 36352255 PMCID: PMC9860053 DOI: 10.1038/s41396-022-01336-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/11/2022]
Abstract
Although microbial decomposition of plant litter plays a crucial role in nutrient cycling and soil fertility, we know less about likely links of specific microbial traits and decomposition, especially in relation to climate change. We study here wheat straw decomposition under ambient and manipulated conditions simulating a future climate scenario (next 80 years) in agroecosystems, including decay rates, macronutrient dynamics, enzyme activity, and microbial communities. We show that future climate will accelerate straw decay rates only during the early phase of the decomposition process. Additionally, the projected climate change will increase the relative abundance of saprotrophic fungi in decomposing wheat straw. Moreover, the impact of future climate on microbial community assembly and molecular ecological networks of both bacteria and fungi will strongly depend on the decomposition phase. During the early phase of straw decomposition, stochastic processes dominated microbial assembly under ambient climate conditions, whereas deterministic processes highly dominated bacterial and fungal communities under simulated future climate conditions. In the later decomposition phase, similar assembly processes shaped the microbial communities under both climate scenarios. Furthermore, over the early phases of decomposition, simulated future climate enhanced the complexity of microbial interaction networks. We concluded that the impact of future climate on straw decay rate and associated microbial traits like assembly processes and inter-community interactions is restricted to the early phase of decomposition.
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Affiliation(s)
- Sara Fareed Mohamed Wahdan
- grid.7492.80000 0004 0492 3830Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany ,grid.33003.330000 0000 9889 5690Department of Botany & Microbiology, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Li Ji
- grid.7492.80000 0004 0492 3830Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany ,grid.440660.00000 0004 1761 0083School of Forestry, Central South University of Forestry and Technology, Changsha, PR China
| | - Martin Schädler
- grid.421064.50000 0004 7470 3956German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany ,grid.7492.80000 0004 0492 3830Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Yu-Ting Wu
- grid.412083.c0000 0000 9767 1257Department of Forestry, National Pingtung University of Science and Technology, Pingtung, Taiwan ,grid.412019.f0000 0000 9476 5696Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Chakriya Sansupa
- grid.7132.70000 0000 9039 7662Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Benjawan Tanunchai
- grid.7492.80000 0004 0492 3830Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - François Buscot
- grid.7492.80000 0004 0492 3830Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany ,grid.421064.50000 0004 7470 3956German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Witoon Purahong
- grid.7492.80000 0004 0492 3830Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
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Gattoni K, Gendron EMS, Borgmeier A, McQueen JP, Mullin PG, Powers K, Powers TO, Porazinska DL. Context-dependent role of abiotic and biotic factors structuring nematode communities along two environmental gradients. Mol Ecol 2022; 31:3903-3916. [PMID: 35593510 DOI: 10.1111/mec.16541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 04/14/2022] [Accepted: 05/17/2022] [Indexed: 11/28/2022]
Abstract
Although abiotic environmental factors have been historically regarded as the dominant deterministic process in microbial community assembly, recent studies indicate that biotic interactions may be equally significant. However, the extent to which both processes are important in assembly of belowground communities is unknown. Along two environmental gradients: alkalinity (ranging from pH ~7 to ~11) and habitat type (lakes, shorelines, and prairies around lakes) present in the Western Nebraska Sandhills, we used 18S rRNA gene marker metabarcoding and statistical analyses, including generalized dissimilarity modelling (GDM), to evaluate the dynamics between abiotic and biotic factors that might play a role in nematode community assembly. Lakes supported the least diverse and prairies the most diverse communities with completely distinct compositions. We also observed a potential role of alkalinity in shaping these communities but only in lakes. Generally, GDMs indicated the influence of both abiotic and biotic factors. However, their relative importance in explaining community variability was dependent on the habitat. Biotic factors influenced the lake communities most, followed by shorelines and prairies, explaining ~47%, 27% and 8% of the variation, respectively. In contrast, the role of abiotic factors was relatively similar in lakes, shorelines and prairies (~15%, 18% and 14% of the variation, respectively). Most variation in the shorelines (62%) and prairies (82%) remained unexplained, suggesting the potential importance of factors associated with specific traits or a stronger role of stochastic processes. Nevertheless, our findings suggest both deterministic processes are important in nematode community assembly, but their specific contributions are context-dependent.
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Affiliation(s)
- Kaitlin Gattoni
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | | | - Abigail Borgmeier
- Department of Plant Pathology, 406 Plant Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - J Parr McQueen
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Peter G Mullin
- Department of Plant Pathology, 406 Plant Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Kris Powers
- Department of Plant Pathology, 406 Plant Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Thomas O Powers
- Department of Plant Pathology, 406 Plant Science, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
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Hu L, Li Q, Yan J, Liu C, Zhong J. Vegetation restoration facilitates belowground microbial network complexity and recalcitrant soil organic carbon storage in southwest China karst region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153137. [PMID: 35041964 DOI: 10.1016/j.scitotenv.2022.153137] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 05/16/2023]
Abstract
Soil organic carbon (SOC) is an important component of soil ecosystems, and soils are a hotbed of microorganisms playing critical roles in soil functions and ecosystem services. Understanding the interaction between SOC and soil microbial community is of paramount significance in predicting the C fate in soils following vegetation restoration. In this study, high-throughput sequencing of 16S rRNA and ITS genes combined with 13C NMR spectroscopy analysis were applied to characterize SOC chemical compounds and elucidate associated soil microbial community. Our results indicated that the contents of SOC, total nitrogen, total phosphorus, microbial biomass carbon and biomass nitrogen, dissolved organic carbon, available potassium, exchangeable calcium and soil moisture increased significantly (P < 0.05) along with the vegetation restoration processes from corn land, grassland, shrub land, to secondary and primary forests. Moreover, the Alkyl C and O-alkyl C abundance increased with vegetation recovery, but no significant differences of Alkyl C were observed in different successional stages. In contrast, the relative abundance of Methoxyl C showed an opposite trend. The dominate phyla Proteobacteria, Acidobacteria, Actinobacteria, Ascomycota and Basidiomycota were strongly related to SOC. And, SOC was found to be the determining factor shaping soil bacterial and fungal communities in vegetation restoration processes. The complexity of soil bacteria and fungi interactions along the vegetation restoration chronosequence increased. Determinism was the major assembly mechanism of bacterial community while stochasticity dominated the assembly of fungal community. Bryobacter, Haliangium, and MND1 were identified as keystone genera in co-occurrence network. Besides, the dominant functional groups across all vegetation restoration processes were mainly involved in soil C and N cycles and linked to the enhanced recalcitrant SOC storage. Our results provide invaluable reference to advance the understanding of microbe response to vegetation restoration processes and highlight the impact of microbes on recalcitrant SOC storage.
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Affiliation(s)
- Linan Hu
- Institute of Groundwater and Earth Sciences, Jinan University, Guangzhou 510632, China; Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China
| | - Qiang Li
- Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China.
| | - Jiahui Yan
- Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China
| | - Chun Liu
- Institute of Groundwater and Earth Sciences, Jinan University, Guangzhou 510632, China; Department of Ecology, Jinan University, Guangzhou 510632, China.
| | - Juxin Zhong
- Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China
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10
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Aleklett K, Rosa D, Pickles BJ, Hart MM. Community Assembly and Stability in the Root Microbiota During Early Plant Development. Front Microbiol 2022; 13:826521. [PMID: 35531294 PMCID: PMC9069014 DOI: 10.3389/fmicb.2022.826521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
Little is known about how community composition in the plant microbiome is affected by events in the life of a plant. For example, when the plant is exposed to soil, microbial communities may be an important factor in root community assembly. We conducted two experiments asking whether the composition of the root microbiota in mature plants could be determined by either the timing of root exposure to microbial communities or priority effects by early colonizing microbes. Timing of microbial exposure was manipulated through an inoculation experiment, where plants of different ages were exposed to a common soil inoculum. Priority effects were manipulated by challenging roots with established microbiota with an exogenous microbial community. Results show that even plants with existing microbial root communities were able to acquire new microbial associates, but that timing of soil exposure affected root microbiota composition for both bacterial and fungal communities in mature plants. Plants already colonized were only receptive to colonizers at 1 week post-germination. Our study shows that the timing of soil exposure in the early life stages of a plant is important for the development of the root microbiota in mature plants.
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Affiliation(s)
- Kristin Aleklett
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomm, Sweden
| | - Daniel Rosa
- Department of Biology, University of British Columbia – Okanagan, Kelowna, BC, Canada
| | - Brian John Pickles
- School of Biological Sciences, University of Reading, Health & Life Sciences Building, Whiteknights, United Kingdom
| | - Miranda M. Hart
- Department of Biology, University of British Columbia – Okanagan, Kelowna, BC, Canada
- *Correspondence: Miranda M. Hart,
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11
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Yang X, You L, Hu H, Chen Y. Conversion of grassland to cropland altered soil nitrogen-related microbial communities at large scales. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151645. [PMID: 34774635 DOI: 10.1016/j.scitotenv.2021.151645] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/18/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Land-use changes may dramatically disturb underground microbial biodiversity, especially in the fragile ecological areas. However, the impact of conversion of grassland to cropland on soil nitrogen (N)-related microbial communities is not fully understood in the farming-pastoral ecotone of northern China. Therefore, 24 paired grassland and cropland soil samples were collected in this region to investigate the community structure and assembly processes of soil N-related microorganisms via amplicon sequencing of nifH, archaeal and bacterial amoA, and nxrB genes. The results showed higher ammonia-oxidizing bacteria (AOB) alpha diversity but a lower nitrite-oxidizing bacteria (NOB) diversity in cropland soil compared to grassland soil. Non-metric multidimensional scaling ordinations revealed that diazotroph, AOB and NOB communities differed considerably between grassland and cropland soil. Soil microbial co-occurrence networks showed that conversion of grassland to cropland significantly lowered the average degree, average clustering coefficient, total nodes and links, resulting in less complex microbial networks in cropland soil. Land-use change altered AOB community assembly processes, resulting from a stochasticity-dominated process in grassland soil to a determinism-dominated process in cropland soil. In contrast, deterministic processes were dominant in diazotroph community assembly, whereas stochastic processes were dominant in constructing ammonia-oxidizing archaea and NOB communities in both grassland and cropland soil. These results provide novel evidence that the conversion of grassland to cropland altered the diversity and assembly processes of soil microbial communities involved in soil N-cycling processes, which has important implications for the potential changes in soil functions under land-use changes.
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Affiliation(s)
- Xue Yang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Luncheng You
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Hangwei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yongliang Chen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China.
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12
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Zhao Y, Guan D, Liu X, Gao GF, Meng F, Liu B, Xing P, Jiang X, Ma M, Cao F, Li L, Li J. Profound Change in Soil Microbial Assembly Process and Co-occurrence Pattern in Co-inoculation of Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 on Soybean. Front Microbiol 2022; 13:846359. [PMID: 35369449 PMCID: PMC8972127 DOI: 10.3389/fmicb.2022.846359] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
Rhizosphere microbial communities are vital for plant growth and soil sustainability; however, the composition of rhizobacterial communities, especially the assembly process and co-occurrence pattern among microbiota after the inoculation of some beneficial bacteria, remains considerably unclear. In this study, we investigated the structure of rhizomicrobial communities, their assembly process, and interactions contrasting when Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 are co-inoculated or Bradyrhizobium japonicum 5038 mono-inoculated in black and cinnamon soils of soybean fields. The obtained results indicated that the Chao and Shannon indices were all higher in cinnamon soil than that in black soil. In black soil, the co-inoculation increased the Shannon indices of bacteria comparing with that of the mono-inoculation. In cinnamon soil, the co-inoculation decreased the Chao indices of fungi comparing with that of mono-inoculation. Compared with the mono-inoculation, the interactions of microorganisms of co-inoculation in the co-occurrence pattern increased in complexity, and the nodes and edges of co-inoculation increased by 10.94, 40.18 and 4.82, 16.91% for bacteria and fungi, respectively. The co-inoculation of Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 increased the contribution of stochastic processes comparing with Bradyrhizobium japonicum 5038 inoculation in the assembly process of soil microorganisms, and owing to the limitation of species diffusion might restrict the direction of pathogenic microorganism movement. These findings support the feasibility of rebuilding the rhizosphere microbial system via specific microbial strain inoculation and provide evidence that the co-inoculation of Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 can be adopted as an excellent compound rhizobia agent resource for the sustainable development of agriculture.
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Affiliation(s)
- Yubin Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Gui-Feng Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Fangang Meng
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Jilin, China
| | - Bingqiang Liu
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Hebei, China
| | - Pengfei Xing
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
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13
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The Changes in Soil Microbial Communities across a Subalpine Forest Successional Series. FORESTS 2022. [DOI: 10.3390/f13020289] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Knowledge regarding changes in soil microbial communities with forest succession is vital to understand soil microbial community shifts under global change scenarios. The composition and diversity of soil microbial communities across a subalpine forest successional series were therefore investigated in the Wanglang National Nature Reserve on the eastern Qinghai-Tibet Plateau, China. The calculated diversity indices of soil bacteria (8.598 to 9.791 for Shannon-Wiener, 0.997 to 0.974 for Simpson, 4131 to 4974 for abundance-based coverage estimator (ACE) and 3007 to 3511 for Species richness indices), and ACE (1323 to 921) and Species richness (1251 to 879) indices of soil fungi decreased from initial to terminal succession stages, but Shannon-Wiener and Simpson of soil fungi indices varied slightly with forest succession. Meanwhile, the composition and structure of soil microbial communities varied markedly with forest succession. The relative abundance of the dominant bacterial phyla (Acidobacteria, Firmicutes and Actinobacteria) and fungal taxa (Mortierellomycota, Rozellomycota and unassigned phylum clade GS01) varied considerably with forest succession. However, regardless of successional stage, Proteobacteria and Acidobacteria dominated soil bacterial communities and Ascomycota and Basidiomycota dominated soil fungal communities. Moreover, the changes in soil microbial diversity with forest succession were significantly affected by soil pH, soil organic carbon, soil temperature, altitude, and non-woody debris stock. Importantly, soil pH was the dominant driver of soil microbial community shift with forest succession. In conclusion, the forests at different succession stages not only conserve same microbial populations, but also nurse unique microbial diversity across the forest succession series; and the biodiversity of soil bacterial and fungal communities has differential responses to forest succession.
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14
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Liu S, Yin H, Li X, Li X, Fan C, Chen G, Feng M, Chen Y. Short-Term Thinning Influences the Rhizosphere Fungal Community Assembly of Pinus massoniana by Altering the Understory Vegetation Diversity. Front Microbiol 2021; 12:620309. [PMID: 33767676 PMCID: PMC7985072 DOI: 10.3389/fmicb.2021.620309] [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: 10/22/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Thinning can significantly promote forest productivity and ecological function. Rhizosphere fungi play an indispensable role in regulating nutrient cycling between plants and the environment, and their community composition can positively respond to anthropogenic disturbance. However, the initial effects of thinning on rhizosphere fungal community assembly have seldom been reported. In this research, we studied the alterations in the rhizosphere fungal communities of 29-year-old Pinus massoniana in East Sichuan 2 years after three different thinning intensity treatments. In addition, the responses of fungal community and functional group composition to alterations in understory vegetation and soil physiochemical properties were analyzed. Three thinning intensities were set, which were 0 (CK), 25% (LIT), and 50% (HIT), respectively. The results suggested that the richness index and Shannon index of understory vegetation increased significantly with increasing thinning intensity. The alpha diversity indices of rhizosphere fungal community and soil physiochemical properties did not show significant differences among the three treatments. The relative abundances of 17 fungal indicator species varied regularly with increasing thinning intensity, and most of them belong to Hypocreales and Eurotiales, indicating that these two orders were potential indicators for different thinning treatments. Rhizosphere fungal community assembly was determined by deterministic process, and it was driven by the diversity of understory vegetation in the initial stage of thinning. The Simpson index and Pielou index of herbs were useful measures of the main environmental factors driving the differentiation of fungal functional group composition. Based on network analysis, thinning resulted in distinct co-occurrence patterns of rhizosphere fungal functional groups. This research elucidates the initial role of thinning in rhizosphere fungal community assembly of P. massoniana and has practical significance for the functional restoration and protection of local forest ecosystem.
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Affiliation(s)
- Size Liu
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Haifeng Yin
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Xiangjun Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Xianwei Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of State Forestry Administration for Forest Resources Conservation and Ecological Security in Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Chuan Fan
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of State Forestry Administration for Forest Resources Conservation and Ecological Security in Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Gang Chen
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of State Forestry Administration for Forest Resources Conservation and Ecological Security in Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Maosong Feng
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of State Forestry Administration for Forest Resources Conservation and Ecological Security in Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yuqin Chen
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of State Forestry Administration for Forest Resources Conservation and Ecological Security in Upper Reaches of Yangtze River, Sichuan Agricultural University, Chengdu, China
- Forestry Ecological Engineering in Upper Reaches of Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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15
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Gao GF, Peng D, Zhang Y, Li Y, Fan K, Tripathi BM, Adams JM, Chu H. Dramatic change of bacterial assembly process and co-occurrence pattern in Spartina alterniflora salt marsh along an inundation frequency gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142546. [PMID: 33035970 DOI: 10.1016/j.scitotenv.2020.142546] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/02/2020] [Accepted: 09/19/2020] [Indexed: 05/20/2023]
Abstract
Exotic Spartina alterniflora has become widely distributed along most of the coastlines in China in a wide range of inundation frequencies. However, the assembly processes and co-occurrence patterns of the bacterial community in S. alterniflora wetlands under different inundation frequencies remain elusive. In this study, an in-situ mesocosm was established to investigate the changes in soil bacterial community. We found that soil water content was the most decisive factor in influencing the bacterial community. Balanced variation, rather than abundance gradients, accounted for the major shifts in bacterial communities and was significantly and positively correlated with the changes in water content, suggesting that species substitution was facilitated by the increased water content. Deterministic processes were dominant in community assembly, and a large degree of change in water content increased variable selection. Co-occurrence network revealed that increasing water content significantly decreased the average degree and the relative abundance of keystone species, resulting in a network with less complexity. Structural equation modelling suggests that increasing inundation frequency has strong impacts on bacterial community, primarily by altering water content, network degree, and the relative abundance of keystone species. Overall, our results illustrate that increasing inundation frequency significantly influences the bacterial community assembly processes and co-occurrence patterns.
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Affiliation(s)
- Gui-Feng Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Dan Peng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Yihui Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Yuntao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Binu M Tripathi
- Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jonathan M Adams
- School of Geography and Ocean Science, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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16
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Aguirre de Cárcer D. Experimental and computational approaches to unravel microbial community assembly. Comput Struct Biotechnol J 2020; 18:4071-4081. [PMID: 33363703 PMCID: PMC7736701 DOI: 10.1016/j.csbj.2020.11.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
Microbial communities have a preponderant role in the life support processes of our common home planet Earth. These extremely diverse communities drive global biogeochemical cycles, and develop intimate relationships with most multicellular organisms, with a significant impact on their fitness. Our understanding of their composition and function has enjoyed a significant thrust during the last decade thanks to the rise of high-throughput sequencing technologies. Intriguingly, the diversity patterns observed in nature point to the possible existence of fundamental community assembly rules. Unfortunately, these rules are still poorly understood, despite the fact that their knowledge could spur a scientific, technological, and economic revolution, impacting, for instance, agricultural, environmental, and health-related practices. In this minireview, I recapitulate the most important wet lab techniques and computational approaches currently employed in the study of microbial community assembly, and briefly discuss various experimental designs. Most of these approaches and considerations are also relevant to the study of microbial microevolution, as it has been shown that it can occur in ecological relevant timescales. Moreover, I provide a succinct review of various recent studies, chosen based on the diversity of ecological concepts addressed, experimental designs, and choice of wet lab and computational techniques. This piece aims to serve as a primer to those new to the field, as well as a source of new ideas to the more experienced researchers.
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17
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Uritskiy G, Munn A, Dailey M, Gelsinger DR, Getsin S, Davila A, McCullough PR, Taylor J, DiRuggiero J. Environmental Factors Driving Spatial Heterogeneity in Desert Halophile Microbial Communities. Front Microbiol 2020; 11:578669. [PMID: 33193201 PMCID: PMC7606970 DOI: 10.3389/fmicb.2020.578669] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/24/2020] [Indexed: 12/22/2022] Open
Abstract
Spatial heterogeneity in microbial communities is observed in all natural ecosystems and can stem from both adaptations to local environmental conditions as well as stochastic processes. Extremophile microbial communities inhabiting evaporitic halite nodules (salt rocks) in the Atacama Desert, Chile, are a good model ecosystem for investigating factors leading to microbiome heterogeneity, due to their diverse taxonomic composition and the spatial segregation of individual nodules. We investigated the abiotic factors governing microbiome composition across different spatial scales, allowing for insight into the factors that govern halite colonization from regional desert-wide scales to micro-scales within individual nodules. We found that water availability and community drift account for microbiome assembly differently at different distance scales, with higher rates of cell dispersion at the smaller scales resulting in a more homogenous composition. This trend likely applies to other endoliths, and to non-desert communities, where dispersion between communities is limited. At the intra-nodule scales, a light availability gradient was most important in determining the distribution of microbial taxa despite intermixing by water displacement via capillary action.
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Affiliation(s)
- Gherman Uritskiy
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Adam Munn
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Micah Dailey
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Diego R. Gelsinger
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Samantha Getsin
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Alfonso Davila
- NASA Ames Research Center, Moffett Field, CA, United States
| | - P. R. McCullough
- Department of Physics and Astronomy, Johns Hopkins University, and Space Telescope Science Institute, Baltimore, MD, United States
| | - James Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
| | - Jocelyne DiRuggiero
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
- Department of Earth & Planetary Sciences, Johns Hopkins University, Baltimore, MD, United States
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18
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Stoof-Leichsenring KR, Dulias K, Biskaborn BK, Pestryakova LA, Herzschuh U. Lake-depth related pattern of genetic and morphological diatom diversity in boreal Lake Bolshoe Toko, Eastern Siberia. PLoS One 2020; 15:e0230284. [PMID: 32294095 PMCID: PMC7159240 DOI: 10.1371/journal.pone.0230284] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/25/2020] [Indexed: 11/19/2022] Open
Abstract
Large, old and heterogenous lake systems are valuable sources of biodiversity. The analysis of current spatial variability within such lakes increases our understanding of the origin and establishment of biodiversity. The environmental sensitivity and the high taxonomic richness of diatoms make them ideal organisms to investigate intra-lake variability. We investigated modern intra-lake diatom diversity in the large and old sub-arctic Lake Bolshoe Toko in Siberia. Our study uses diatom-specific metabarcoding, applying a short rbcL marker combined with next-generation sequencing and morphological identification to analyse the diatom diversity in modern sediment samples of 17 intra-lake sites. We analysed abundance-based compositional taxonomic diversity and generic phylogenetic diversity to investigate the relationship of diatom diversity changes with water depth. The two approaches show differences in taxonomic identification and alpha diversity, revealing a generally higher diversity with the genetic approach. With respect to beta diversity and ordination analyses, both approaches result in similar patterns. Water depth or related lake environmental conditions are significant factors influencing intra-lake diatom patterns, showing many significant negative correlations between alpha and beta diversity and water depth. Further, one near-shore and two lagoon lake sites characterized by low (0-10m) and medium (10-30m) water depth are unusual with unique taxonomic compositions. At deeper (>30m) water sites we identified strongest phylogenetic clustering in Aulacoseira, but generally much less in Staurosira, which supports that water depth is a strong environmental filter on the Aulacoseira communities. Our study demonstrates the utility of combining analyses of genetic and morphological as well as phylogenetic diversity to decipher compositional and generic phylogenetic patterns, which are relevant in understanding intra-lake heterogeneity as a source of biodiversity in the sub-arctic glacial Lake Bolshoe Toko.
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Affiliation(s)
- Kathleen R. Stoof-Leichsenring
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Katharina Dulias
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Boris K. Biskaborn
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Luidmila A. Pestryakova
- Department of Geography and Biology, North-Eastern Federal University of Yakutsk, Yakutsk, Russia
| | - Ulrike Herzschuh
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
- Institute of Environmental Science and Geography, University of Potsdam, Potsdam, Germany
- Institute of Biology and Biochemistry, University of Potsdam, Potsdam, Germany
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