1
|
Kayiranga A, Isabwe A, Yao H, Shangguan H, Coulibaly JLK, Breed M, Sun X. Distribution patterns of soil bacteria, fungi, and protists emerge from distinct assembly processes across subcommunities. Ecol Evol 2024; 14:e11672. [PMID: 38988351 PMCID: PMC11236429 DOI: 10.1002/ece3.11672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 07/12/2024] Open
Abstract
Environmental change exerts a profound effect on soil microbial domains-including bacteria, fungi, and protists-that each perform vital ecological processes. While these microbial domains are ubiquitous and extremely diverse, little is known about how they respond to environmental changes in urban soil ecosystems and what ecological processes shape them. Here we investigated the community assembly processes governing bacteria, fungi, and protists through the lens of four distinct subcommunities: abundant, conditionally rare, conditionally abundant, and rare taxa. We show that transient taxa, including the conditionally rare and conditionally rare or abundant taxa, were the predominant subcommunities. Deterministic processes (e.g., environmental filtering) had major roles in structuring all subcommunities of fungi, as well as conditionally rare and abundant protists. Stochastic processes had strong effects in structuring all subcommunities of bacteria (except rare taxa) and conditionally rare protists. Overall, our study underscores the importance of complementing the traditional taxonomy of microbial domains with the subcommunity approach when investigating microbial communities in urban soil ecosystems.
Collapse
Affiliation(s)
- Alexis Kayiranga
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Alain Isabwe
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
| | - Haifeng Yao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Huayuan Shangguan
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Justin Louis Kafana Coulibaly
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| | - Martin Breed
- College of Science and Engineering Flinders University Bedford Park South Australia Australia
| | - Xin Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment Chinese Academy of Sciences Xiamen China
- University of Chinese Academy of Sciences Beijing China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control CAS Haixi Industrial Technology Innovation Center in Beilun Ningbo China
| |
Collapse
|
2
|
Mendonca C, Zhang L, Waldbauer JR, Aristilde L. Disproportionate Carbon Dioxide Efflux in Bacterial Metabolic Pathways for Different Organic Substrates Leads to Variable Contribution to Carbon-Use Efficiency. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11041-11052. [PMID: 38860668 PMCID: PMC11210201 DOI: 10.1021/acs.est.4c01328] [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: 02/04/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024]
Abstract
Microbial organic matter turnover is an important contributor to the terrestrial carbon dioxide (CO2) budget. Partitioning of organic carbons into biomass relative to CO2 efflux, termed carbon-use efficiency (CUE), is widely used to characterize organic carbon cycling by soil microorganisms. Recent studies challenge proposals of CUE dependence on the oxidation state of the substrate carbon and implicate instead metabolic strategies. Still unknown are the metabolic mechanisms underlying variability in CUE. We performed a multiomics investigation of these mechanisms in Pseudomonas putida, a versatile soil bacterium of the Gammaproteobacteria, processing a mixture of plant matter derivatives. Our 13C-metabolomics data captured substrate carbons into different metabolic pathways: cellulose-derived sugar carbons in glycolytic and pentose-phosphate pathways; lignin-related aromatic carbons in the tricarboxylic acid cycle. Subsequent 13C-metabolic flux analysis revealed a 3-fold lower investment of sugar carbons in CO2 efflux compared to aromatic carbons, in agreement with reported substrate-dependent CUE. Proteomics analysis revealed enzyme-level regulation only for substrate uptake and initial catabolism, which dictated downstream fluxes through CO2-producing versus biomass-synthesizing reactions. Metabolic partitioning as shown here explained the substrate-dependent CUE calculated from reported metabolic flux analyses of other bacteria, further supporting a metabolism-guided perspective for predicting the microbial conversion of accessible organic matter to CO2 efflux.
Collapse
Affiliation(s)
- Caroll
M. Mendonca
- Department
of Biological and Environmental Engineering, College of Agriculture
and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department
of Civil and Environmental Engineering, McCormick School of Engineering
and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Lichun Zhang
- Department
of the Geophysical Sciences, University
of Chicago, Chicago, Illinois 60637, United States
| | - Jacob R. Waldbauer
- Department
of the Geophysical Sciences, University
of Chicago, Chicago, Illinois 60637, United States
| | - Ludmilla Aristilde
- Department
of Biological and Environmental Engineering, College of Agriculture
and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department
of Civil and Environmental Engineering, McCormick School of Engineering
and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
3
|
Hu Y, Zhang H, Sun X, Zhang B, Wang Y, Rafiq A, Jia H, Liang C, An S. Impact of grassland degradation on soil multifunctionality: Linking to protozoan network complexity and stability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172724. [PMID: 38663601 DOI: 10.1016/j.scitotenv.2024.172724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
Soil protozoa, as predators of microbial communities, profoundly influence multifunctionality of soils. Understanding the relationship between soil protozoa and soil multifunctionality (SMF) is crucial to unraveling the driving mechanisms of SMF. However, this relationship remains unclear, particularly in grassland ecosystems that are experiencing degradation. By employing 18S rRNA gene sequencing and network analysis, we examined the diversity, composition, and network patterns of the soil protozoan community along a well-characterized gradient of grassland degradation at four alpine sites, including two alpine meadows (Cuona and Jiuzhi) and two alpine steppes (Shuanghu and Gonghe) on the Qinghai-Tibetan Plateau. Our findings showed that grassland degradation decreased SMF for 1-2 times in all four sites but increased soil protozoan diversity (Shannon index) for 13.82-298.01 % in alpine steppes. Grassland degradation-induced changes in soil protozoan composition, particularly to the Intramacronucleata with a large body size, were consistently observed across all four sites. The enhancing network complexity (average degree), stability (robustness), and cooperative relationships (positive correlation) are the responses of protozoa to grassland degradation. Further analyses revealed that the increased network complexity and stability led to a decrease in SMF by affecting microbial biomass. Overall, protozoa increase their diversity and strengthen their cooperative relationships to resist grassland degradation, and emphasize the critical role of protozoan network complexity and stability in regulating SMF. Therefore, not only protozoan diversity and composition but also their interactions should be considered in evaluating SMF responses to grassland degradation, which has important implications for predicting changes in soil function under future scenarios of anthropogenic change.
Collapse
Affiliation(s)
- Yang Hu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China; College of Resources and Environment, Xinjiang Agricultural University, Urumqi 830052, China
| | - Haolin Zhang
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Xinya Sun
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Bicheng Zhang
- Institute of Soil and Water Conservation, CAS & MWR, Yangling, Shannxi 712100, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Yubin Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Anum Rafiq
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Hongtao Jia
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi 830052, China
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China.
| |
Collapse
|
4
|
Li H, Wang Z, Feng B, Shi J, Liao M, He K, Tian H, Megharaj M, He W. Arsenic stress on soil microbial nutrient metabolism interpreted by microbial utilization of dissolved organic carbon. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134232. [PMID: 38593666 DOI: 10.1016/j.jhazmat.2024.134232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/11/2024]
Abstract
In a 120-day microcosm incubation experiment, we investigated the impact of arsenic contamination on soil microbial nutrient metabolism, focusing on carbon cycling processes. Our study encompassed soil basal respiration, key enzyme activities (particularly, β-1,4-N-acetylglucosaminidase and phosphatases), microbial biomass, and community structure. Results revealed a substantial increase (1.21-2.81 times) in β-1,4-N-acetylglucosaminidase activities under arsenic stress, accompanied by a significant decrease (9.86%-45.20%) in phosphatase activities (sum of acid and alkaline phosphatases). Enzymatic stoichiometry analysis demonstrated the mitigation of microbial C and P requirements in response to arsenic stress. The addition of C-sources alleviated microbial C requirements but exacerbated P requirements, with the interference amplitude increasing with the complexity of the C-source. Network analysis unveiled altered microbial nutrient requirements and an increased resistance process of microbes under arsenic stress. Microbial carbon use efficiency (CUE) and basal respiration significantly increased (1.17-1.59 and 1.18-3.56 times, respectively) under heavy arsenic stress (500 mg kg-1). Arsenic stress influenced the relative abundances of microbial taxa, with Gemmatimonadota increasing (5.5-50.5%) and Bacteroidota/ Nitrospirota decreasing (31.4-47.9% and 31.2-63.7%). Application of C-sources enhanced microbial resistance to arsenic, promoting cohesion among microorganisms. These findings deepen our understanding of microbial nutrient dynamics in arsenic-contaminated areas, which is crucial for developing enzyme-based toxicity assessment systems for soil arsenic contamination.
Collapse
Affiliation(s)
- Huayong Li
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Ziquan Wang
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Bingcong Feng
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Jing Shi
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Maoyuan Liao
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Kangming He
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Haixia Tian
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Wenxiang He
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China.
| |
Collapse
|
5
|
Yang N, Li Y, Lin L, Niu L, Zhang W, Wang L. Transition of organic matter from allochthonous to autochthonous alters benthic nutrient dynamics via microbial food webs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170186. [PMID: 38278244 DOI: 10.1016/j.scitotenv.2024.170186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/08/2024] [Accepted: 01/13/2024] [Indexed: 01/28/2024]
Abstract
The impoundment of rivers by dams has significantly modified sedimentation patterns and trophic structures. As a result, the algal-derived organic matter (OM), as opposed to terrestrial-derived OM, plays an increasingly important role along the river-reservoir gradient. This study utilized water-sediment microcosms to explore the impacts of allochthonous and autochthonous OM deposition on benthic nutrient dynamics mediated by microbial food webs. Our results revealed that OM addition led to increased fluxes of NH4+ and CO2, with the highest flux induced by cyanobacteria OM, followed by diatom and allochthonous OM. N2 release flux was promoted by allochthonous and diatom OM deposition but inhibited by cyanobacteria OM deposition. The amendment of autochthonous OM increased the activity of dehydrogenase and urease, while allochthonous OM with a higher C/N ratio enhanced the catalytic abilities of polyphenol oxidase and β-glucosidase. Furthermore, OM deposition significantly reduced microbial community richness and diversity, except for eukaryotic richness, and induced pronounced changes in bacterial and eukaryotic community structures. Allochthonous OM deposition stimulated the utilization of bacteria and protozoan on native OM, resulting in a positive priming effect of 26.78 %. In contrast, diatom and cyanobacteria OM additions exerted negative priming effects of -44.53 % and -29.76 %, respectively. Bayesian stable isotope mixing models showed that diatom OM was primarily absorbed by protozoan and metazoan, while cyanobacteria OM was more easily decomposed by bacteria and transferred to higher trophic levels through microbial food webs. In addition, bacterial ammonification accounted for 74.5 % of NH4+ release in the allochthonous OM deposition treatment, whereas eukaryotic excretion contributed separately 83.3 % and 83.1 % to NH4+ release in the diatom and cyanobacteria OM addition treatments. These findings highlight the significance of accounting for the regulatory capacity of OM deposition when studying benthic metabolism within river-reservoir systems.
Collapse
Affiliation(s)
- Nan Yang
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, PR China; College of Geography and Remote Sensing, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- College of Hydrology and Water Resources, Hohai University, Nanjing 210098, PR China.
| | - Li Lin
- Key Laboratory of Basin Water Resource and Eco-Environmental Science in Hubei Province, Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Wuhan 430010, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| |
Collapse
|
6
|
He X, Xiao X, Wei W, Li L, Zhao Y, Zhang N, Wang M. Soil rare microorganisms mediated the plant cadmium uptake: The central role of protists. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168505. [PMID: 37967623 DOI: 10.1016/j.scitotenv.2023.168505] [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: 08/22/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023]
Abstract
Plants and microorganisms symbiotically mediate and/or catalyse the turnover of elements in rhizosphere soils, thus directly influencing the effectiveness of phytoremediation in addressing heavy metal contamination. Soil rare microbial communities are diverse but not well understood in terms of their importance for phytoremediation. In this study, we simulated the loss of rare microorganisms through dilution-to-extinction approach, and investigated the effects on integrated rhizosphere microbiome with soil microcosm experiments, including bacteria, fungi, protists, and microfauna. Additionally, we explored the implications for ryegrass (Lolium multiflorum Lam.) growth and its uptake of Cd (cadmium). Compared with the undiluted group, ryegrass exhibited a significant decrease in Cd uptake ranging from 52.34 % to 73.71 % in the rare species-loss soils, indicating a lack of functional redundancy in rhizosphere soil microbial community following rare species loss. Interestingly, these soils displayed a remarkable 1.79-fold increase in plant biomass and a 41.02 % increase in plant height. By sequencing the 16S, 18S, and ITS rRNA gene amplicons of rhizosphere microbes, we found that soil rare species loss decreased the rhizosphere microbial α-diversity, changed the community structures, and shifted the functional potential. Protists were particularly affected. Through the analysis of species co-occurrence networks, along with the partial least squares path modeling, we found that the diversity of protists and bacteria and the co-occurring network connectivity of protists and fungi contributed most to plant Cd uptake and growth. These results highlighted the potential significance of rare microorganisms, particularly protists, in phytoextraction of Cd-contaminated soils, owing to their central role in the microbial food web.
Collapse
Affiliation(s)
- Xingguo He
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China
| | - Xian Xiao
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China.
| | - Weiwei Wei
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Liangzhong Li
- Chongqing Huanyue Ecological Environment Technology Co., Ltd., Chongqing 400000, China
| | - Yuan Zhao
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China
| | - Na Zhang
- Hunan Soil and Fertilizer Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Mingyu Wang
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China
| |
Collapse
|
7
|
Li A, Li A, Luo C, Liu B. Assessing heavy metal contamination in Amomum villosum Lour. fruits from plantations in Southern China: Soil-fungi-plant interactions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 269:115789. [PMID: 38091669 DOI: 10.1016/j.ecoenv.2023.115789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 11/14/2023] [Accepted: 12/03/2023] [Indexed: 01/12/2024]
Abstract
Amomum villosum Lour. fruit is a common healthy food widely cultivated in southern China. Heavy metal contamination of farmland soils has becomes a serious environmental concern in China. Heavy metals in soil can be introduced into the food chain and pose health risks to humans. However, microbial communities may play beneficial roles in plants grown in metal-polluted soils. This study aimed to assess the potential health risks of heavy metals in soils and A. villosum fruits from different production areas and to explore the soil-microbe-plant regulation pattern for heavy metals in A. villosum fruits. Soil and A. villosum fruit samples were collected from nine planting fields in four provinces of southern China. The results showed that soils from seven areas were polluted with heavy metals to different degrees. Cr and Mn were the most serious contaminating elements. However, the accumulation of heavy metals in A. villosum fruit was negligible with no expected human health risks. Partial least squares path analysis of structural equation modeling showed that the accumulation of heavy metals in A. villosum fruits was influenced by multiple factors. More importantly, the PLS-SEM revealed that the heavy metal content in A. villosum fruits was indirectly affected by soil heavy metals through the regulation of the microbial community. Furthermore, some fungal phyla (e.g., Ascomycota and Chytridiomycota) and genera (e.g., Mucor) were related to the heavy metal content in the soil and in A. villosum fruits. The results of this study verified that soil fungal community play an important role in the accumulation of heavy metals in A. villosum fruits. Using fungi provides a potential biological strategy for reducing the health risk posed by heavy metals in food.
Collapse
Affiliation(s)
- Arong Li
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510006, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Aqian Li
- School of Psychology, South China Normal University, 510631 Guangzhou, China
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Bo Liu
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510006, China; Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou 510006, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangzhou 510006, China.
| |
Collapse
|
8
|
Likar M, Grašič M, Stres B, Regvar M, Gaberščik A. Metagenomics reveals effects of fluctuating water conditions on functional pathways in plant litter microbial community. Sci Rep 2023; 13:21741. [PMID: 38066117 PMCID: PMC10709317 DOI: 10.1038/s41598-023-49044-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
Climate change modifies environmental conditions, resulting in altered precipitation patterns, moisture availability and nutrient distribution for microbial communities. Changes in water availability are projected to affect a range of ecological processes, including the decomposition of plant litter and carbon cycling. However, a detailed understanding of microbial stress response to drought/flooding is missing. In this study, an intermittent lake is taken up as a model for changes in water availability and how they affect the functional pathways in microbial communities of the decomposing Phragmites australis litter. The results show that most enriched functions in both habitats belonged to the classes of Carbohydrates and Clustering-based subsystems (terms with unknown function) from SEED subsystems classification. We confirmed that changes in water availability resulted in altered functional makeup of microbial communities. Our results indicate that microbial communities under more frequent water stress (due to fluctuating conditions) could sustain an additional metabolic cost due to the production or uptake of compatible solutes to maintain cellular osmotic balance. Nevertheless, although prolonged submergence seemed to have a negative impact on several functional traits in the fungal community, the decomposition rate was not affected.
Collapse
Affiliation(s)
- Matevž Likar
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia.
| | - Mateja Grašič
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Blaž Stres
- Institute of Sanitary Engineering, Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia
- Biocybernetics and Robotics, Department of Automation, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marjana Regvar
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Alenka Gaberščik
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia
| |
Collapse
|
9
|
Hakobyan A, Velte S, Sickel W, Quandt D, Stoll A, Knief C. Tillandsia landbeckii phyllosphere and laimosphere as refugia for bacterial life in a hyperarid desert environment. MICROBIOME 2023; 11:246. [PMID: 37936139 PMCID: PMC10631034 DOI: 10.1186/s40168-023-01684-x] [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: 06/15/2023] [Accepted: 09/28/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND The lack of water is a major constraint for microbial life in hyperarid deserts. Consequently, the abundance and diversity of microorganisms in common habitats such as soil are strongly reduced, and colonization occurs primarily by specifically adapted microorganisms that thrive in particular refugia to escape the harsh conditions that prevail in these deserts. We suggest that plants provide another refugium for microbial life in hyperarid deserts. We studied the bacterial colonization of Tillandsia landbeckii (Bromeliaceae) plants, which occur in the hyperarid regions of the Atacama Desert in Chile, one of the driest and oldest deserts on Earth. RESULTS We detected clear differences between the bacterial communities being plant associated to those of the bare soil surface (PERMANOVA, R2 = 0.187, p = 0.001), indicating that Tillandsia plants host a specific bacterial community, not only dust-deposited cells. Moreover, the bacterial communities in the phyllosphere were distinct from those in the laimosphere, i.e., on buried shoots (R2 = 0.108, p = 0.001), indicating further habitat differentiation within plant individuals. The bacterial taxa detected in the phyllosphere are partly well-known phyllosphere colonizers, but in addition, some rather unusual taxa (subgroup2 Acidobacteriae, Acidiphilum) and insect endosymbionts (Wolbachia, "Candidatus Uzinura") were found. The laimosphere hosted phyllosphere-associated as well as soil-derived taxa. The phyllosphere bacterial communities showed biogeographic patterns across the desert (R2 = 0.331, p = 0.001). These patterns were different and even more pronounced in the laimosphere (R2 = 0.467, p = 0.001), indicating that different factors determine community assembly in the two plant compartments. Furthermore, the phyllosphere microbiota underwent temporal changes (R2 = 0.064, p = 0.001). CONCLUSIONS Our data demonstrate that T. landbeckii plants host specific bacterial communities in the phyllosphere as well as in the laimosphere. Therewith, these plants provide compartment-specific refugia for microbial life in hyperarid desert environments. The bacterial communities show biogeographic patterns and temporal variation, as known from other plant microbiomes, demonstrating environmental responsiveness and suggesting that bacteria inhabit these plants as viable microorganisms. Video Abstract.
Collapse
Affiliation(s)
- Anna Hakobyan
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Stefanie Velte
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Wiebke Sickel
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
- Institute of Biodiversity, Johann Heinrich Von Thünen Institute, Brunswick, Germany
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas Ceaza, La Serena, Chile
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - Claudia Knief
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany.
| |
Collapse
|
10
|
Jiang R, Wang M, Chen W. Heavy metal pollution triggers a shift from bacteria-based to fungi-based soil micro-food web: Evidence from an abandoned mining-smelting area. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132164. [PMID: 37598513 DOI: 10.1016/j.jhazmat.2023.132164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 08/22/2023]
Abstract
Heavy metals pose significant threats to soil biota, ultimately disrupting soil micro-food web. However, no studies have yet elucidated the impact of heavy metals on soil micro-food web. In this study, we explored the response of bacteria, fungi, nematodes, and soil micro-food web along a gradient of heavy metals in an abandoned smelting-mining area. We found that bacteria responded strongly to heavy metals, whereas fungi showed greater resistance and tolerance. Nematodes responses were less apparent. With the increasing levels of heavy metal pollution, the importance of heavy metal-tolerant organisms in micro-food webs increased significantly. For instance, the keystone bacteria in soil micro-food web shifted from copiotrophic to oligotrophic types, while the keystone nematodes shifted from to bacterial-feeding (e.g., Eucephalobus) to fungal-feeding species (e.g., Ditylenchus). Additionally, elevated heavy metal concentrations increased the proportion of fungi (e.g., Mortierellomycota), intensifying their interactions with bacteria and nematodes and causing a shift from bacteria-based to fungi-based soil micro-food web. Furthermore, heavy metal contamination induced a more complex and stable soil micro-food web. Overall, we highlight the changes in soil micro-food web as a mechanism for coping with heavy metal stress. Our study provides valuable insights into how heavy metal pollution can cause shifts in soil micro-food webs and has critical implications for enhancing our understanding of the ecological consequences of environmental pollution at the ecosystem level.
Collapse
Affiliation(s)
- Rong Jiang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Meie Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049,China.
| | - Weiping Chen
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049,China
| |
Collapse
|
11
|
Hartmann M, Herzog C, Brunner I, Stierli B, Meyer F, Buchmann N, Frey B. Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition. Front Microbiol 2023; 14:1267270. [PMID: 37840720 PMCID: PMC10570739 DOI: 10.3389/fmicb.2023.1267270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Climate change can alter the flow of nutrients and energy through terrestrial ecosystems. Using an inverse climate change field experiment in the central European Alps, we explored how long-term irrigation of a naturally drought-stressed pine forest altered the metabolic potential of the soil microbiome and its ability to decompose lignocellulolytic compounds as a critical ecosystem function. Drought mitigation by a decade of irrigation stimulated profound changes in the functional capacity encoded in the soil microbiome, revealing alterations in carbon and nitrogen metabolism as well as regulatory processes protecting microorganisms from starvation and desiccation. Despite the structural and functional shifts from oligotrophic to copiotrophic microbial lifestyles under irrigation and the observation that different microbial taxa were involved in the degradation of cellulose and lignin as determined by a time-series stable-isotope probing incubation experiment with 13C-labeled substrates, degradation rates of these compounds were not affected by different water availabilities. These findings provide new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest and will help to improve our understanding of alterations in biogeochemical cycling under a changing climate.
Collapse
Affiliation(s)
- Martin Hartmann
- Department of Environmental Systems Science, Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Claude Herzog
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Folker Meyer
- Data Science, Institute for AI in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Argonne National Laboratory, Argonne, IL, United States
- Computation Institute, University of Chicago, Chicago, IL, United States
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | - Nina Buchmann
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| |
Collapse
|
12
|
Yin Y, Wang X, Hu Y, Li F, Cheng H. Insights on the assembly processes and drivers of soil microbial communities in different depth layers in an abandoned polymetallic mining district. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:132043. [PMID: 37453349 DOI: 10.1016/j.jhazmat.2023.132043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/02/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Soil microbes, which play crucial roles in maintaining soil functions and restoring degraded lands, are impacted by heavy metal pollution. This study investigated the vertical distribution of bacterial communities along the soil profiles across four types of areas (heavy metal pollution level: tailings heap area > phytoremediation area > natural restoration area > original forest area) in an abandoned polymetallic mining district by 16S rRNA sequencing, and aimed to disentangle the assembly mechanisms and key drivers of the vertical variation in bacterial community structure. Bacterial diversity and composition were found to vary remarkably between the depth layers in all types of areas, with heterogeneous selection dominated the vertical distribution pattern of soil bacterial communities. Pearson correlation analysis and partial Mantel test revealed that soil nutrients mainly shaped the vertical distribution of bacterial microbiota along soil profiles in the original forest and natural restoration areas. Ni, As, and bioavailable As were the key drivers regulating the vertical variation of bacterial assemblages in the phytoremediation area, whereas Pb, pH, soil organic carbon, and available nitrogen were crucial drivers in the tailings heap area. These findings reveal the predominant assembly mechanisms and drivers governing the vertical distribution of soil bacterial microbiota and indicate the efficiency of phytoremediation and ecological restoration on ameliorating edaphic micro-ecosystems in heavy metal-contaminated areas.
Collapse
Affiliation(s)
- Yue Yin
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Xiaojie Wang
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yuanan Hu
- MOE Laboratory of Groundwater Circulation and Evolution, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fadong Li
- State Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|
13
|
McGuire PM, Butkevich N, Saksena AV, Walter MT, Shapleigh JP, Reid MC. Oxic-anoxic cycling promotes coupling between complex carbon metabolism and denitrification in woodchip bioreactors. Environ Microbiol 2023; 25:1696-1712. [PMID: 37105180 DOI: 10.1111/1462-2920.16387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023]
Abstract
Denitrifying woodchip bioreactors (WBRs) are increasingly used to manage the release of non-point source nitrogen (N) by stimulating microbial denitrification. Woodchips serve as a renewable organic carbon (C) source, yet the recalcitrance of organic C in lignocellulosic biomass causes many WBRs to be C-limited. Prior studies have observed that oxic-anoxic cycling increased the mobilization of organic C, increased nitrate (NO3 - ) removal rates, and attenuated production of nitrous oxide (N2 O). Here, we use multi-omics approaches and amplicon sequencing of fungal 5.8S-ITS2 and prokaryotic 16S rRNA genes to elucidate the microbial drivers for enhanced NO3 - removal and attenuated N2 O production under redox-dynamic conditions. Transient oxic periods stimulated the expression of fungal ligninolytic enzymes, increasing the bioavailability of woodchip-derived C and stimulating the expression of denitrification genes. Nitrous oxide reductase (nosZ) genes were primarily clade II, and the ratio of clade II/clade I nosZ transcripts during the oxic-anoxic transition was strongly correlated with the N2 O yield. Analysis of metagenome-assembled genomes revealed that many of the denitrifying microorganisms also have a genotypic ability to degrade complex polysaccharides like cellulose and hemicellulose, highlighting the adaptation of the WBR microbiome to the ecophysiological niche of the woodchip matrix.
Collapse
Affiliation(s)
- Philip M McGuire
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - Natalie Butkevich
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - Aryaman V Saksena
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - M Todd Walter
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - James P Shapleigh
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Matthew C Reid
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| |
Collapse
|
14
|
Prosenkov A, Cagnon C, Gallego JLR, Pelaez AI. The microbiome of a brownfield highly polluted with mercury and arsenic. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121305. [PMID: 36804142 DOI: 10.1016/j.envpol.2023.121305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.
Collapse
Affiliation(s)
- Alexander Prosenkov
- Area of Microbiology, Department of Functional Biology, Environmental Biogeochemistry and Raw Materials Group and IUBA, University of Oviedo, 33006 Oviedo, Asturias, Spain
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - José Luis R Gallego
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, Campus of Mieres, University of Oviedo, 33600 Mieres, Asturias, Spain
| | - Ana Isabel Pelaez
- Area of Microbiology, Department of Functional Biology, Environmental Biogeochemistry and Raw Materials Group and IUBA, University of Oviedo, 33006 Oviedo, Asturias, Spain.
| |
Collapse
|
15
|
Wu CM, Wheeler KM, Cárcamo-Oyarce G, Aoki K, McShane A, Datta SS, Mark Welch JL, Tiemeyer M, Griffen AL, Ribbeck K. Mucin glycans drive oral microbial community composition and function. NPJ Biofilms Microbiomes 2023; 9:11. [PMID: 36959210 PMCID: PMC10036478 DOI: 10.1038/s41522-023-00378-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/20/2023] [Indexed: 03/25/2023] Open
Abstract
Human microbiome composition is closely tied to health, but how the host manages its microbial inhabitants remains unclear. One important, but understudied, factor is the natural host environment: mucus, which contains gel-forming glycoproteins (mucins) that display hundreds of glycan structures with potential regulatory function. Leveraging a tractable culture-based system to study how mucins influence oral microbial communities, we found that mucin glycans enable the coexistence of diverse microbes, while resisting disease-associated compositional shifts. Mucins from tissues with unique glycosylation differentially tuned microbial composition, as did isolated mucin glycan libraries, uncovering the importance of specific glycan patterns in microbiome modulation. We found that mucins shape microbial communities in several ways: serving as nutrients to support metabolic diversity, organizing spatial structure through reduced aggregation, and possibly limiting antagonism between competing taxa. Overall, this work identifies mucin glycans as a natural host mechanism and potential therapeutic intervention to maintain healthy microbial communities.
Collapse
Affiliation(s)
- Chloe M Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kelsey M Wheeler
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gerardo Cárcamo-Oyarce
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kazuhiro Aoki
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Abigail McShane
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sujit S Datta
- Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | | | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Ann L Griffen
- Department of Dentistry, Nationwide Children's Hospital, Columbus, OH, USA
- Divisions of Biosciences and Pediatric Dentistry, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
16
|
Teng T, Liang J, Wu Z, Jin P, Zhang D. Different phenanthrene degraders between free-cell mediated and biochar-immobilization assisted soil bioaugmentation as identified by RNA-based stable isotope probing (RNA-SIP). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161139. [PMID: 36572297 DOI: 10.1016/j.scitotenv.2022.161139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/04/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Bioaugmentation (BA) is an effective approach to remove polycyclic aromatic hydrocarbons (PAHs) from contaminated soils, and biochar is frequently used to enhance PAH degradation performance. In this study, phenanthrene (PHE) degradation behavior and active degraders in a petroleum-contaminated soil were investigated and compared between free-cell mediated and biochar-immobilization assisted bioaugmentation. Biochar-immobilization assisted bioaugmentation (BA-IPB) introduced PHE degraders immobilized on biochar and effectively promoted PHE degradation, achieving higher PHE removal efficiencies within 24 h (~58 %) than free-cell mediated bioaugmentation (BA-FPB, ~39 %). Soil microbial community structure significantly changed in both BA-FPB and BA-IPB treatments. Through RNA-stable isotope probing (SIP), 14 and 11 bacterial lineages responsible for in situ PHE degradation were identified in BA-FPB and BA-IPB treatments, respectively. ASV_17 in BA-FPB treatment was Rhodococcus in the exogenous bacterial mixture; in contrast, none of exogenous bacteria were involved in PHE degradation in BA-IPB treatment. Methylobacterium (ASV_186), Xanthomonas (ASV_41), Kroppenstedtia (ASV_205), Scopulibacillus (ASV_243), Bautia (ASV_356), and Lactobacillus (ASV_376) were identified as PHE degraders for the first time. Our findings expanded the knowledge of the active PHE degraders and underlying mechanisms in bioaugmentation process, and suggested biochar-immobilization assisted bioaugmentation as a promising strategy for the bioremediation of PAH contaminated soils.
Collapse
Affiliation(s)
- Tingting Teng
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University, Xi'an 710000, PR China; College of New Energy and Environment, Jilin University, Changchun 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Jidong Liang
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University, Xi'an 710000, PR China.
| | - Zijun Wu
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University, Xi'an 710000, PR China
| | - Pengkang Jin
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University, Xi'an 710000, PR China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun 130021, PR China
| |
Collapse
|
17
|
Active predation, phylogenetic diversity, and global prevalence of myxobacteria in wastewater treatment plants. THE ISME JOURNAL 2023; 17:671-681. [PMID: 36774445 PMCID: PMC9919749 DOI: 10.1038/s41396-023-01378-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/13/2023]
Abstract
The operation of modern wastewater treatment plants (WWTPs) is driven by activated sludge microbiota, a complex assemblage of trophically interacting microorganisms. Microbial predation is crucial to fundamental understanding of how biological interactions drive microbiome structuring and functioning of WWTPs. However, predatory bacteria have received little attention regarding their diversity, activity, and ecological function in activated sludge, limiting the exploitation of food web interactions for wastewater microbiome engineering. Here, by using rRNA-stable isotope probing of activated sludge microbiota with 13C-labeled prey bacteria, we uncovered diverse as-yet-uncultivated putative predatory bacteria that actively incorporated 13C-biomass. Myxobacteria, especially Haliangium and the mle1-27 clade, were found as the dominant active predators, refreshing conventional views based on a few predatory isolates of Bdellovibrionota from WWTPs. The identified predatory bacteria showed more selective predation on prey compared with the protists dominated by ciliates, providing in situ evidence for inter-domain predation behavior divergence in activated sludge. Putative predatory bacteria were tracked over a two-year microbiome monitoring effort at a local WWTP, revealing the predominance of Myxococcota (6.5 ± 1.3%) over Bdellovibrionota (1.0 ± 0.2%) lineages. Phylogenetic analysis unveiled highly diverse myxobacteria inhabiting activated sludge and suggested a habitat filtering effect in global WWTPs. Further mining of a global activated sludge microbiome dataset revealed the prevalence of Myxococcota (5.4 ± 0.1%) species and potential impacts of myxobacterial predation on process performance. Collectively, our findings provided unique insights into the predating activity, diversity, and prevalence of Myxococcota species in activated sludge, highlighting their links with wastewater treatment processes via trophic regulation of enteric and functional bacteria.
Collapse
|
18
|
Soil Chemistry and Soil History Significantly Structure Oomycete Communities in Brassicaceae Crop Rotations. Appl Environ Microbiol 2023; 89:e0131422. [PMID: 36629416 PMCID: PMC9888183 DOI: 10.1128/aem.01314-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Oomycetes are critically important in soil microbial communities, especially for agriculture, where they are responsible for major declines in yields. Unfortunately, oomycetes are vastly understudied compared to bacteria and fungi. As such, our understanding of how oomycete biodiversity and community structure vary through time in the soil remains poor. Soil history established by previous crops is one factor known to structure other soil microbes, but this has not been investigated for its influence on oomycetes. In this study, we established three different soil histories in field trials; the following year, these plots were planted with five different Brassicaceae crops. We hypothesized that the previously established soil histories would structure different oomycete communities, regardless of their current Brassicaceae crop host, in both the roots and rhizosphere. We used a nested internal transcribed spacer amplicon strategy incorporated with MiSeq metabarcoding, where the sequencing data was used to infer amplicon sequence variants of the oomycetes present in each sample. This allowed us to determine the impact of different soil histories on the structure and biodiversity of the oomycete root and rhizosphere communities from the five different Brassicaceae crops. We found that each soil history structured distinct oomycete rhizosphere communities, regardless of different Brassicaceae crop hosts, while soil chemistry structured the oomycete communities more during a dry year. Interestingly, soil history appeared specific to oomycetes but was less influential for bacterial communities previously identified from the same samples. These results advance our understanding of how different agricultural practices and inputs can alter edaphic factors to impact future oomycete communities. Examining how different soil histories endure and impact oomycete biodiversity will help clarify how these important communities may be assembled in agricultural soils. IMPORTANCE Oomycetes cause global plant diseases that result in substantial losses, yet they are highly understudied compared to other microbes, like fungi and bacteria. We wanted to investigate how past soil events, like changing crops in rotation, would impact subsequent oomycete communities. We planted different oilseed crops in three different soil histories and found that each soil history structured a distinct oomycete community regardless of which new oilseed crop was planted, e.g., oomycete communities from last year's lentil plots were still detected the following year regardless of which new oilseed crops we planted. This study demonstrated how different agricultural practices can impact future microbial communities differently. Our results also highlight the need for continued monitoring of oomycete biodiversity and quantification.
Collapse
|
19
|
Zhang X, Huang Z, Zhong Z, Li Q, Bian F, Yang C. Metagenomic insights into the characteristics of soil microbial communities in the decomposing biomass of Moso bamboo forests under different management practices. Front Microbiol 2022; 13:1051721. [PMID: 36590390 PMCID: PMC9797724 DOI: 10.3389/fmicb.2022.1051721] [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: 09/23/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Considering the rapid growth and high biomass productivity, Moso bamboo (Phyllostachys edulis) has high carbon (C) sequestration potential, and different management practices can strongly modify its C pools. Soil microorganisms play an important role in C turnover through dead plant and microbial biomass degradation. To date, little is known about how different management practices affect microbial carbohydrate-active enzymes (CAZymes) and their responses to dead biomass degradation. Methods Based on metagenomics analysis, this study analyzed CAZymes in three comparable stands from each Moso bamboo plantation: undisturbed (M0), extensively managed (M1), and intensively managed (M2). Results The results showed that the number of CAZymes encoding plant-derived component degradation was higher than that encoding microbe-derived component degradation. Compared with the M0, the CAZyme families encoding plant-derived cellulose were significantly (p < 0.05) high in M2 and significantly (p < 0.05) low in M1. For microbe-derived components, the abundance of CAZymes involved in the bacterial-derived peptidoglycan was higher than that in fungal-derived components (chitin and glucans). Furthermore, M2 significantly increased the fungal-derived chitin and bacterial-derived peptidoglycan compared to M0, whereas M1 significantly decreased the fungal-derived glucans and significantly increased the bacterial-derived peptidoglycan. Four bacterial phyla (Acidobacteria, Actinobacteria, Proteobacteria, and Chloroflexi) mainly contributed to the degradation of C sources from the plant and microbial biomass. Redundancy analysis (RDA) and mantel test suggested the abundance of CAZyme encoding genes for plant and microbial biomass degradation are significantly correlated with soil pH, total P, and available K. Least Squares Path Modeling (PLS-PM) showed that management practices indirectly affect the CAZyme encoding genes associated with plant and microbial biomass degradation by regulating the soil pH and nutrients (total N and P), respectively. Discussion Our study established that M2 and M1 impact dead biomass decomposition and C turnover, contributing to decreased C accumulation and establishing that the bacterial community plays the main role in C turnover in bamboo plantations.
Collapse
Affiliation(s)
- Xiaoping Zhang
- Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, China National Bamboo Research Center, Zhejiang, China,National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Zhejiang, China,Engineering Research Center of Biochar of Zhejiang Province, Zhejiang, China
| | - Zhiyuan Huang
- Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, China National Bamboo Research Center, Zhejiang, China,National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Zhejiang, China
| | - Zheke Zhong
- Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, China National Bamboo Research Center, Zhejiang, China,National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Zhejiang, China,*Correspondence: Zheke Zhong,
| | - Qiaoling Li
- Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, China National Bamboo Research Center, Zhejiang, China,National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Zhejiang, China
| | - Fangyuan Bian
- Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, China National Bamboo Research Center, Zhejiang, China,National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Zhejiang, China
| | - Chuanbao Yang
- Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, China National Bamboo Research Center, Zhejiang, China,National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Zhejiang, China
| |
Collapse
|
20
|
Yang R, Sun W, Guo L, Li B, Wang Q, Huang D, Gao W, Xu R, Li Y. Response of soil protists to antimony and arsenic contamination. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 315:120387. [PMID: 36223853 DOI: 10.1016/j.envpol.2022.120387] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/07/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Microorganisms can mediate antimony (Sb) and arsenic (As) transformation and thus change their mobility and toxicity. Having similar geochemical behavior, Sb and As are generally considered to exert similar environmental pressure on microbiome. However, it needs further validation, especially for protists. In this study, the responses of protistan communities to Sb and As were investigated by collecting soils from Xikuangshan Sb mine and Shimen As mine in China. Antimony and As contamination taxonomically and functionally (consumer and phototroph) changed the alpha and beta diversities of protistan communities, but exerted different impacts on the parasitic community. Based on multiple statistical tools, As contamination had a greater impact on protistan communities than Sb. The ecological networks of highly contaminated sites were less complex but highly positively connected compared to less contaminated sites. High As contamination raised the ratio of consumers and decreased the ratio of phototrophs in ecological networks, while the opposite tendency was observed in Sb contaminated soils. High Sb and As contamination enriched different keystone taxa resistant to Sb and As. These results demonstrate that protistan community respond differently to Sb and As.
Collapse
Affiliation(s)
- Rui Yang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou, 510650, PR China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou, 510650, PR China
| | - Lifang Guo
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou, 510650, PR China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou, 510650, PR China
| | - Qi Wang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou, 510650, PR China
| | - Duanyi Huang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou, 510650, PR China
| | - Wenlong Gao
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou, 510650, PR China; Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, PR China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, 571737, PR China
| | - Rui Xu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou, 510650, PR China; Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Yongbin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangdong Academy of Sciences, Guangzhou, 510650, PR China.
| |
Collapse
|
21
|
Teng T, Liang J, Zhu J, Jin P, Zhang D. Altered active pyrene degraders in biosurfactant-assisted bioaugmentation as revealed by RNA stable isotope probing. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120192. [PMID: 36126767 DOI: 10.1016/j.envpol.2022.120192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Bioaugmentation is an effective approach for removing pyrene from contaminated sites, and its performance is enhanced by a biosurfactant. To reveal the mechanisms of biosurfactant-assisted bioaugmentation, we introduced RNA stable isotope probing (RNA-SIP) in the pyrene-contaminated soils and explored the impacts of rhamnolipid on the pyrene degradation process. After 12-day degradation, residual pyrene was the lowest in the bioaugmentation treatment (7.76 ± 1.57%), followed by biosurfactant-assisted bioaugmentation (9.86 ± 2.58%) and enhanced natural attenuation (23.97 ± 1.05%). Thirteen well-known and two novel pyrene-degrading bacteria were confirmed to participate in the pyrene degradation. Pyrene degradation was accelerated in the biosurfactant-assisted bioaugmentation, manifested by the high diversity of active pyrene degraders. Our findings expand the knowledge on pyrene degrading bacteria and the mechanisms of pyrene degradation in a bioaugmentation process.
Collapse
Affiliation(s)
- Tingting Teng
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co.,Ltd and Xi'an Jiaotong University, Xi'an, 710049, PR China; College of New Energy and Environment, Jilin University, Changchun, 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun, 130021, PR China
| | - Jidong Liang
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co.,Ltd and Xi'an Jiaotong University, Xi'an, 710049, PR China.
| | - Jinwei Zhu
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co.,Ltd and Xi'an Jiaotong University, Xi'an, 710049, PR China; Shaanxi Electrical Equipment Institute, Xi'an, 710025, PR China
| | - Pengkang Jin
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co.,Ltd and Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun, 130021, PR China
| |
Collapse
|
22
|
Li Y, Gao P, Sun X, Li B, Guo L, Yang R, Su X, Gao W, Xu Z, Yan G, Wang Q, Sun W. Primary Succession Changes the Composition and Functioning of the Protist Community on Mine Tailings, Especially Phototrophic Protists. ACS ENVIRONMENTAL AU 2022; 2:396-408. [PMID: 37101458 PMCID: PMC10125303 DOI: 10.1021/acsenvironau.1c00066] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Primary succession in mine tailings is a prerequisite for tailing vegetation. Microorganisms, including bacteria, fungi, and protists, play an important role in this process in the driving force for improving the nutritional status. Compared to bacteria and fungi, protist populations have rarely been investigated regarding their role in mine tailings, especially for those inhabiting tailings associated with primary succession. Protists are the primary consumers of fungi and bacteria, and their predatory actions promote the release of nutrients immobilized in the microbial biomass, as well as the uptake and turnover of nutrients, affecting the functions of the wider ecosystems. In this study, three different types of mine tailings associated with three successional stages (original tailings, biological crusts, and Miscanthus sinensis grasslands) were selected to characterize the protistan community diversity, structure, and function during primary succession. Some members classified as consumers dominated the network of microbial communities in the tailings, especially in the original bare land tailings. The keystone phototrophs of Chlorophyceae and Trebouxiophyceae showed the highest relative abundance in the biological crusts and grassland rhizosphere, respectively. In addition, the co-occurrences between protist and bacterial taxa demonstrated that the proportion of protistan phototrophs gradually increased during primary succession. Further, the metagenomic analysis of protistan metabolic potential showed that abundances of many functional genes associated with photosynthesis increased during the primary succession of tailings. Overall, these results suggest that the primary succession of mine tailings drives the changes observed in the protistan community, and in turn, the protistan phototrophs facilitate the primary succession of tailings. This research offers an initial insight into the changes in biodiversity, structure, and function of the protistan community during ecological succession on tailings.
Collapse
Affiliation(s)
- Yongbin Li
- National−Regional
Joint Engineering Research Center for Soil Pollution Control and Remediation
in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management,
Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Pin Gao
- National−Regional
Joint Engineering Research Center for Soil Pollution Control and Remediation
in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management,
Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaoxu Sun
- National−Regional
Joint Engineering Research Center for Soil Pollution Control and Remediation
in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management,
Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Baoqin Li
- National−Regional
Joint Engineering Research Center for Soil Pollution Control and Remediation
in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management,
Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Lifang Guo
- National−Regional
Joint Engineering Research Center for Soil Pollution Control and Remediation
in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management,
Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Rui Yang
- National−Regional
Joint Engineering Research Center for Soil Pollution Control and Remediation
in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management,
Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xianfa Su
- School
of Environment, Key Laboratory of Yellow River and Huai River Water
Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, P.R. China
| | - Wenlong Gao
- National−Regional
Joint Engineering Research Center for Soil Pollution Control and Remediation
in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management,
Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Zhimin Xu
- Engineering
and Technology Research Center for Agricultural Land Pollution Prevention
and Control of Guangdong Higher Education Institutes, College of Resources
and Environment, Zhongkai University of
Agriculture and Engineering, Guangzhou 510225, China
| | - Geng Yan
- National−Regional
Joint Engineering Research Center for Soil Pollution Control and Remediation
in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management,
Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Qi Wang
- National−Regional
Joint Engineering Research Center for Soil Pollution Control and Remediation
in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management,
Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Weimin Sun
- National−Regional
Joint Engineering Research Center for Soil Pollution Control and Remediation
in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management,
Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- School
of Environment, Key Laboratory of Yellow River and Huai River Water
Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, P.R. China
- . Fax: 86-020-87024123. Phone: 86-020-87024633
| |
Collapse
|
23
|
Afridi MS, Fakhar A, Kumar A, Ali S, Medeiros FHV, Muneer MA, Ali H, Saleem M. Harnessing microbial multitrophic interactions for rhizosphere microbiome engineering. Microbiol Res 2022; 265:127199. [PMID: 36137486 DOI: 10.1016/j.micres.2022.127199] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/02/2022] [Accepted: 09/13/2022] [Indexed: 10/14/2022]
Abstract
The rhizosphere is a narrow and dynamic region of plant root-soil interfaces, and it's considered one of the most intricate and functionally active ecosystems on the Earth, which boosts plant health and alleviates the impact of biotic and abiotic stresses. Improving the key functions of the microbiome via engineering the rhizosphere microbiome is an emerging tool for improving plant growth, resilience, and soil-borne diseases. Recently, the advent of omics tools, gene-editing techniques, and sequencing technology has allowed us to unravel the entangled webs of plant-microbes interactions, enhancing plant fitness and tolerance to biotic and abiotic challenges. Plants secrete signaling compounds with low molecular weight into the rhizosphere, that engage various species to generate a massive deep complex array. The underlying principle governing the multitrophic interactions of the rhizosphere microbiome is yet unknown, however, some efforts have been made for disease management and agricultural sustainability. This review discussed the intra- and inter- microbe-microbe and microbe-animal interactions and their multifunctional roles in rhizosphere microbiome engineering for plant health and soil-borne disease management. Simultaneously, it investigates the significant impact of immunity utilizing PGPR and cover crop strategy in increasing rhizosphere microbiome functions for plant development and protection using omics techniques. The ecological engineering of rhizosphere plant interactions could be used as a potential alternative technology for plant growth improvement, sustainable disease control management, and increased production of economically significant crops.
Collapse
Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil.
| | - Ali Fakhar
- Division of Applied Science, Gyeongsang National University, South Korea
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | - Sher Ali
- NMR Lab, Department of Chemistry, Federal University of Paraná, Curitiba 81530-900, PR, Brazil
| | - Flavio H V Medeiros
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil
| | - Muhammad Atif Muneer
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hina Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA
| |
Collapse
|
24
|
Miao Y, Lin Y, Chen Z, Zheng H, Niu Y, Kuzyakov Y, Liu D, Ding W. Fungal key players of cellulose utilization: Microbial networks in aggregates of long-term fertilized soils disentangled using 13C-DNA-stable isotope probing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 832:155051. [PMID: 35390367 DOI: 10.1016/j.scitotenv.2022.155051] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/07/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Long-term compost application accelerates organic carbon (C) accumulation and macroaggregate formation in soil. Stable aggregates and high soil organic C (SOC) content are supposed to increase microbiota activity and promote transformation of litter compounds (i.e., cellulose) into SOC. Here, we used 13C-DNA-stable isotope probing with subsequent high-throughput sequencing to characterize fungal succession and co-occurrence trends during 13C-cellulose decomposition in aggregate size classes in soils subjected to no fertilizer (control), nitrogen-phosphorus‑potassium (NPK) fertilizers, and compost (Compost) application for 27 years. Ascomycota (mostly saprotrophic fungi) were always highly competitive for cellulose in all aggregate size classes at the early stages of cellulose decomposition (20 days). Compost-treated soil was enriched with Ascomycota compared to the control soil, wherein Sordariomycetes, the majority, strongly dominated the cellulose utilization (13C incorporation in DNA). 13C-labeled fungal communities converged in the Compost soil, with lower abundance and diversity compared with the NPK and control soils. Such convergence led to greater cellulose decomposition, indicating that compost amendment increased the capacity of a few dominant fungal taxa to decompose litter. Compost soil had more 13C-labeled fungal decomposers in microaggregates and lower fungal decomposers in macroaggregates when compared with the levels in the NPK and control soils. This implies that compost application facilitates fungal colonization towards smaller aggregates. Fungal interactions were reinforced in microaggregates (<250 μm), with more positive associations than those in macroaggregates (>250 μm), indicating greater fungal synergism for recalcitrant resource utilization in microaggregates. The keystone taxa in the co-occurrence networks were not related to cellulose decomposition in microaggregates, but did in macroaggregates. The findings advance a process-based understanding of cellulose utilization by fungal key players based on C and energy availability and the regulation of microbial activity at the aggregate level.
Collapse
Affiliation(s)
- Yuncai Miao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongxin Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zengming Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Huijie Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhui Niu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Büsgenweg 2, Göttingen 37077, Germany; Agro-Technological Institute, RUDN University, 117198 Moscow, Russia
| | - Deyan Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| |
Collapse
|
25
|
Orozco-Mosqueda MDC, Fadiji AE, Babalola OO, Glick BR, Santoyo G. Rhizobiome engineering: Unveiling complex rhizosphere interactions to enhance plant growth and health. Microbiol Res 2022; 263:127137. [PMID: 35905581 DOI: 10.1016/j.micres.2022.127137] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/17/2022] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.
Collapse
Affiliation(s)
| | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico.
| |
Collapse
|
26
|
Zhou X, Sun H, Heinonsalo J, Pumpanen J, Berninger F. Microbial biodiversity contributes to soil carbon release: A case study on fire disturbed boreal forests. FEMS Microbiol Ecol 2022; 98:6617588. [PMID: 35749564 PMCID: PMC9303362 DOI: 10.1093/femsec/fiac074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/10/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial communities often possess enormous diversity, raising questions about whether this diversity drives ecosystem functioning, especially the influence of diversity on soil decomposition and respiration. Although functional redundancy is widely observed in soil microorganisms, evidence that species occupy distinct metabolic niches has also emerged. In this paper, we found that apart from the environmental variables, increases in microbial diversity, notably bacterial diversity, lead to an increase in soil C emissions. This was demonstrated using structural equation modelling (SEM), linking soil respiration with naturally differing levels of soil physio-chemical properties, vegetation coverage, and microbial diversity after fire disturbance. Our SEMs also revealed that models including bacterial diversity explained more variation of soil CO2 emissions (about 45%) than fungal diversity (about 38%). A possible explanation of this discrepancy is that fungi are more multifunctional than bacteria and, therefore, an increase in fungal diversity does not necessarily change soil respiration. Further analysis on functional genes suggested that bacterial and fungal diversities mainly explain the potential decomposition of recalcitrant C than of labile C. Overall, by incorporating microbial diversity and the environmental variables, the predictive power of models on soil C emission was significantly improved, indicating microbial diversity is crucial for predicting ecosystem functions.
Collapse
Affiliation(s)
- Xuan Zhou
- Department of Environmental and Biological Sciences, Joensuu campus, University of Eastern Finland, 80101, Joensuu, Finland
| | - Hui Sun
- Collaborative Innovation Center of Sustainable Forestry in China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China
| | - Jussi Heinonsalo
- Department of Forest Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Jukka Pumpanen
- Department of Environmental and Biological Sciences, Joensuu campus, University of Eastern Finland, 80101, Joensuu, Finland
| | - Frank Berninger
- Department of Environmental and Biological Sciences, Joensuu campus, University of Eastern Finland, 80101, Joensuu, Finland
| |
Collapse
|
27
|
Chen J, Yang Y, Ke Y, Chen X, Jiang X, Chen C, Xie S. Anaerobic sulfamethoxazole-degrading bacterial consortia in antibiotic-contaminated wetland sediments identified by DNA-stable isotope probing and metagenomics analysis. Environ Microbiol 2022; 24:3751-3763. [PMID: 35688651 DOI: 10.1111/1462-2920.16091] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022]
Abstract
Anaerobic degradation has been demonstrated as an important pathway for the removal of sulfonamide (SA) in contaminated environments, and identifying the microorganisms responsible for the degradation of SA is a key step in developing bioaugmentation approaches. In this study, we investigated the anaerobic degradation activity of three SA [sulfadiazine (SDZ), sulfamethazine (SMZ) and sulfamethoxazole (SMX)] and the associated bacterial community in wetland sediments contaminated by aquaculture (in Fujian Province, coded with FJ), livestock farming (in Sichuan Province, coded with SC), or rural wastewaters (in Guangdong Province, coded with GD). Additionally, the combination of DNA-stable isotope probing (SIP) with metagenomics was further applied to assess the active SA-degrading microbes using SMX as a model SA. Among SDZ, SMZ and SMX, only SMX could be effectively dissipated, and the degradation of SMX was relatively fast in the microcosms of sediments with higher levels of SA contamination (FJ and SC). The anaerobic biotransformation pathway of SMX was initiated by hydrogenation with the cleavage of the N-O bond on the isoxazole ring. DNA-SIP revealed that the in situ active anaerobic SMX-degraders (5, 18 and 3 genera in sediments FJ, SC and GD respectively) were dominated by Proteobacteria in sediments FJ and SC, but by Firmicutes (two Family XVIII members) in sediment GD. Mycobacterium, unclassified Burkholderiaceae and Rhodocyclaceae were identified as the dominant active SMX-degrading bacteria in both sediments FJ and SC. Higher proportions of antibiotic resistance gene and genes involved in various functional categories were observed in sediments FJ and SC.
Collapse
Affiliation(s)
- Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Yuyin Yang
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment (MEE), Guangzhou, 510655, China
| | - Yanchu Ke
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Xinshu Jiang
- State Key Joint Laboratory of Environment Simulation and Pollution Control (SKJLESPC), Beijing Key Laboratory for Emerging Organic Contaminants Control (BKLEOC), School of Environment, POPs Research Center, Tsinghua University, Beijing, 100084, China
| | - Chao Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| |
Collapse
|
28
|
Li Y, Yang R, Guo L, Gao W, Su P, Xu Z, Xiao H, Ma Z, Liu X, Gao P, Li B, Sun X, Yan G, Sun W. The composition, biotic network, and assembly of plastisphere protistan taxonomic and functional communities in plastic-mulching croplands. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128390. [PMID: 35152106 DOI: 10.1016/j.jhazmat.2022.128390] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
The increasing use of plastic film mulching has caused the accumulation of plastic film residue in soil. To date, most researches on the plastisphere have focused on bacterial and fungal communities, with few on protistan community, especially in terrestrial ecosystems. To understand plastisphere protistan communities, we collected plastic film residues from plastic-mulching croplands. The plastisphere significantly altered the alpha-diversity, structure, and composition of taxonomic and functional (consumers, phototrophs, and parasites) communities. In both the plastisphere and surrounding soil, although some consumers dominated the protistan community network, while their performance was weakened by mulch application. The ecological networks of the plastisphere community presented higher modularity, less complexity, and a lower proportion of positive connections than the networks of surrounding soil. In addition, the enriched plant pathogens (e.g., Spongospora) and keystone taxa classified as plant pathogens (e.g., Pythium) in the plastisphere imply that plastic film residues may pose a risk to soil health and plant performance. Neutral-based processes dominated the assembly of the plastisphere protistan communities, whereas niche-based processes governed the protistan community assembly of surrounding soil. This study reveals that plastic film residues generate a unique niche for protistan colonization, which disturbs protistan communities and threatens agricultural ecosystem health and function.
Collapse
Affiliation(s)
- Yongbin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Rui Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Lifang Guo
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Wenlong Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Pingzhou Su
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Zhimin Xu
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Huan Xiao
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Zhixiong Ma
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xiang Liu
- Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control of Guangdong Higher Education Institutes, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Geng Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China.
| |
Collapse
|
29
|
Long-Term Compost Amendment Spurs Cellulose Decomposition by Driving Shifts in Fungal Community Composition and Promoting Fungal Diversity and Phylogenetic Relatedness. mBio 2022; 13:e0032322. [PMID: 35491853 PMCID: PMC9239258 DOI: 10.1128/mbio.00323-22] [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] [Indexed: 11/25/2022] Open
Abstract
Cellulose is the most abundant polysaccharide in plant biomass and an important precursor of soil organic matter formation. Fungi play a key role in carbon cycling dynamics because they tend to decompose recalcitrant materials. Here, we applied [12C]cellulose and [13C]cellulose to distinguish the effects of application of compost, nitrogen-phosphorus-potassium (NPK) fertilizer, and no fertilizer (control) for 27 years upon cellulose decomposition via RNA-based stable isotope probing (RNA-SIP). The loss ratio of added cellulose C in compost soil was 67.6 to 106.7% higher than in NPK and control soils during their 20-day incubation. Dothideomycetes (mainly members of the genus Cryptococcus) dominated cellulose utilization in compost soil, whereas the copiotrophic Sordariomycetes were more abundant in NPK and unfertilized soils. Compared with NPK and control soils, compost application increased the diversity of 13C-assimilating fungi. The 13C-labeled fungal communities in compost soil were more phylogenetically clustered and exhibited greater species relatedness than those in NPK and control soils, perhaps because of stringent filtering of narrow-spectrum organic resources and biological invasion originating from added compost. These changes led to an augmented decomposition capacity of fungal species for cellulose-rich substrates and reduced cellulose C sequestration efficiency. The RNA-SIP technique is more sensitive to responses of fungi to altered soil resource availability than DNA-SIP. Overall, long-term compost application modified fungal community composition and promoted fungal diversity and phylogenetic relatedness, accelerating the decomposition of substrate cellulose in soil. This work also highlights the RNA-SIP technique’s value for comprehensively assessing the contributions of active fungi to the substrate decomposition process.
Collapse
|
30
|
Li Y, Wang C, Chen S. Biofertilization containing
Paenibacillus triticisoli
BJ‐18 alters the composition and interaction of the protistan community in the wheat rhizosphere under field conditions. J Appl Microbiol 2022; 132:3746-3757. [DOI: 10.1111/jam.15485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/13/2022] [Accepted: 02/08/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Yongbin Li
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences China Agricultural University Beijing People’s Republic of China
| | - Caixia Wang
- National‐Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro‐environmental Pollution Control and Management Institute of Eco‐environmental and Soil Sciences Guangdong Guangzhou China
| | - Sanfeng Chen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences China Agricultural University Beijing People’s Republic of China
| |
Collapse
|
31
|
Potapov AM, Beaulieu F, Birkhofer K, Bluhm SL, Degtyarev MI, Devetter M, Goncharov AA, Gongalsky KB, Klarner B, Korobushkin DI, Liebke DF, Maraun M, Mc Donnell RJ, Pollierer MM, Schaefer I, Shrubovych J, Semenyuk II, Sendra A, Tuma J, Tůmová M, Vassilieva AB, Chen T, Geisen S, Schmidt O, Tiunov AV, Scheu S. Feeding habits and multifunctional classification of soil‐associated consumers from protists to vertebrates. Biol Rev Camb Philos Soc 2022; 97:1057-1117. [DOI: 10.1111/brv.12832] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 12/17/2022]
Affiliation(s)
- Anton M. Potapov
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Frédéric Beaulieu
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri‐Food Canada Ottawa ON K1A 0C6 Canada
| | - Klaus Birkhofer
- Department of Ecology Brandenburg University of Technology Karl‐Wachsmann‐Allee 6 03046 Cottbus Germany
| | - Sarah L. Bluhm
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Maxim I. Degtyarev
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Miloslav Devetter
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Anton A. Goncharov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Konstantin B. Gongalsky
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Bernhard Klarner
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Daniil I. Korobushkin
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Dana F. Liebke
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Mark Maraun
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Rory J. Mc Donnell
- Department of Crop and Soil Science Oregon State University Corvallis OR 97331 U.S.A
| | - Melanie M. Pollierer
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Ina Schaefer
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Julia Shrubovych
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
- Institute of Systematics and Evolution of Animals PAS Slawkowska 17 Pl 31‐016 Krakow Poland
- State Museum Natural History of NAS of Ukraine Teatralna 18 79008 Lviv Ukraine
| | - Irina I. Semenyuk
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
- Joint Russian‐Vietnamese Tropical Center №3 Street 3 Thang 2, Q10 Ho Chi Minh City Vietnam
| | - Alberto Sendra
- Colecciones Entomológicas Torres‐Sala, Servei de Patrimoni Històric, Ajuntament de València València Spain
- Departament de Didàctica de les Cièncias Experimentals i Socials, Facultat de Magisteri Universitat de València València Spain
| | - Jiri Tuma
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
- Biology Centre CAS, Institute of Entomology Branisovska 1160/31 370 05 Ceske Budejovice Czech Republic
| | - Michala Tůmová
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Anna B. Vassilieva
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Ting‐Wen Chen
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Stefan Geisen
- Department of Nematology Wageningen University & Research 6700ES Wageningen The Netherlands
| | - Olaf Schmidt
- UCD School of Agriculture and Food Science University College Dublin Belfield Dublin 4 Ireland
| | - Alexei V. Tiunov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
- Centre of Biodiversity and Sustainable Land Use Büsgenweg 1 37077 Göttingen Germany
| |
Collapse
|
32
|
Effect of AM Fungi Inoculation on Litter Bacterial Community Characteristics under Heavy Metal Stress. Microorganisms 2022; 10:microorganisms10020206. [PMID: 35208661 PMCID: PMC8879951 DOI: 10.3390/microorganisms10020206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 11/19/2022] Open
Abstract
Because microorganisms are the primary driving force behind litter decomposition, they play an important role in maintaining ecosystem material and chemical cycling. Arbuscular mycorrhizal (AM) fungi can improve host plant tolerance to various environmental stressors, making their application in mining area remediation important. In this study, litter from the dominant plant species (Imperata cylindrica) in a copper tailings mining area was selected as the experimental material. We conducted a greenhouse-based heavy metal stress experiment to investigate how AM fungi affect litter microbial community characteristics and key ecological factors. Results showed that AM fungi species, heavy metal treatments, and their combined interaction had significant impacts on litter pH. Additionally, enzyme activities in litter were significantly affected by interactions between AM fungi species and heavy metal contaminates. Ralstonia was significantly positively correlated to lead (Pb) content, indicating that Ralstonia had a certain tolerance to Pb pollution. Sucrase and urease activity were increased when plants were inoculated with Rhizophagus irregularis under Pb stress. Furthermore, Microbacterium, Brevundimonas, and Pseudonocardia all may play important roles in litter decomposition, while a certain tolerance was observed in Kushneria and Roseivivax to heavy metal pollution when plants were inoculated with Glomus mosseae. Results showed that AM fungi affected litter bacterial community structure and function by influencing plant litter properties. By exploring interactions between AM fungi and bacterial communities in plant litter under heavy metal stress, we will better understand associative processes that promote the cycling of soil organic matter and nutrients contaminated by non-ferrous metal tailings.
Collapse
|
33
|
Dopheide A, Davis C, Nuñez J, Rogers G, Whitehead D, Grelet GA. Depth-structuring of multi-kingdom soil communities in agricultural pastures. FEMS Microbiol Ecol 2021; 97:6447534. [PMID: 34864997 DOI: 10.1093/femsec/fiab156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/29/2021] [Indexed: 12/27/2022] Open
Abstract
The biodiversity and structure of deep agricultural soil communities are poorly understood, especially for eukaryotes. Using DNA metabarcoding and co-occurrence networks, we tested whether prokaryote, fungal, protist, and nematode biodiversity declines with increasing depth (0-0.1, 0.3-0.5, and 1.1-1.7m) in pastoral soil; whether deep soil organisms are subsets of those at the surface; and whether multi-kingdom networks become more interconnected with increasing depth. Depth-related richness declines were observed for almost all detected fungal classes, protist phyla, and nematode orders, but only 13 of 25 prokaryote phyla, of which nine had increasing richness with depth. Deep soil communities were not simply subsets of surface communities, with 3.8%-12.2% of eukaryotes and 13.2% of prokaryotes detected only in the deepest samples. Eukaryotes mainly occurred in the upper soil layers whereas prokaryotes were more evenly distributed across depths. Plant-feeding nematodes were most abundant in top soil, whereas bacteria feeders were more abundant in deep soil. Co-occurrence network structure differences suggested that deep soil communities are concentrated around scarce niches of resource availability, in contrast to more spatially homogenous and abundant resources at the surface. Together, these results demonstrate effects of depth on the composition, distribution, and structure of prokaryote and eukaryote soil communities.
Collapse
Affiliation(s)
- Andrew Dopheide
- Manaaki Whenua-Landcare Research, 231 Morrin Road, St Johns, Auckland 1072, New Zealand
| | - Carina Davis
- Manaaki Whenua-Landcare Research, 54 Gerald Street, Lincoln 7608, New Zealand
| | - Jonathan Nuñez
- Manaaki Whenua-Landcare Research, 54 Gerald Street, Lincoln 7608, New Zealand.,School of Biological Sciences, University of Canterbury, 20 Kirkwood Avenue, Upper Riccarton, Christchurch 8041, New Zealand
| | - Graeme Rogers
- Manaaki Whenua-Landcare Research, 54 Gerald Street, Lincoln 7608, New Zealand
| | - David Whitehead
- Manaaki Whenua-Landcare Research, 54 Gerald Street, Lincoln 7608, New Zealand
| | - Gwen-Aëlle Grelet
- Manaaki Whenua-Landcare Research, 54 Gerald Street, Lincoln 7608, New Zealand
| |
Collapse
|
34
|
Teng T, Liang J, Wu Z. Identification of pyrene degraders via DNA-SIP in oilfield soil during natural attenuation, bioaugmentation and biostimulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149485. [PMID: 34392205 DOI: 10.1016/j.scitotenv.2021.149485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 06/13/2023]
Abstract
Pyrene is a model contaminant of high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs), which are compounds that have potential carcinogenic effects and pose a serious threat to human health. Finding effective pyrene-degrading bacteria is crucial for removing PAHs from soil. In this study, DNA-based stable isotope probing (DNA-SIP) technology was used to investigate pyrene degraders in PAH-contaminated oilfield soil during natural attenuation (NA), bioaugmentation (BA) and biostimulation (BS). The results show that BA played an important role in pyrene degradation with the highest pyrene removal rate (~95%) after 12 days incubation, followed by removal rates of ~90% for NA and ~30% for BS. In addition, 6 novel pyrene degraders were identified, while 12 well-known PAH degraders were demonstrated to participate in the biodegradation of pyrene. Additionally, the external homologous strains introduced during BA promoted the degradation of pyrene, but not by directly participating in the metabolism of the target compound. Rhamnolipid supplementation during BS promoted the involvement of more microorganisms in the degradation of pyrene, which was beneficial to identifying more pyrene degraders via DNA-SIP. These findings provide new insight into the effects of external homologous strains and supplementary rhamnolipids on pyrene degradation.
Collapse
Affiliation(s)
- Tingting Teng
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jidong Liang
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Zijun Wu
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| |
Collapse
|
35
|
Chen H, Yin C, Fan X, Ye M, Liang Y. Effect of P availability on straw-induced priming effect was mainly regulated by fungi in croplands. Appl Microbiol Biotechnol 2021; 105:9403-9418. [PMID: 34837124 DOI: 10.1007/s00253-021-11691-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 01/16/2023]
Abstract
Phosphorus (P) accumulation in croplands resulting from ever-increasing input of P fertilizer strongly influences soil microbial growth and activities, which is expected to alter the soil priming effect (PE) induced by plant residue. However, the effect of P availability on the magnitude and direction of PE remains largely unexplored and the underlying microbial mechanisms are still unclear. Therefore, a 40-day incubation experiment was established by adding C4-maize straw to C3-soils with or without long-term P fertilizer inputs to investigate PE and accompanied dynamics of microbiota. The results revealed that in both soils, straw application caused positive real PEs via a "microbial co-metabolism" mechanism, accompanied by a microbial succession from the dominance of r- and K-strategists to K-strategists (mainly fungi). In addition, long-term amendment with P increased PE by 83.2% compared with no P fertilization control, which was mainly mediated by K-strategists, especially the fungal families Chaetomiaceae and Myrmecridiaceae. The increased PE was accompanied by enhanced microbial biomass carbon, extracellular enzyme activities, and bacterial gene abundance, confirming the "stoichiometric decomposition" theory. Meanwhile, deviating from the conventional paradigm, higher phosphatase activity and lower enzymatic stoichiometry of carbon (C)-to-P ratios in high-P soil compared with that in low-P soil suggested stronger "P mining" with high-P availability.
Collapse
Affiliation(s)
- Hao Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chang Yin
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoping Fan
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Mujun Ye
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yongchao Liang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|
36
|
de Andrade Reis RJ, Alves AF, Dos Santos PHD, Aguiar KP, da Rocha LO, da Silveira SF, Canellas LP, Olivares FL. Mutualistic interaction of native Serratia marcescens UENF-22GI with Trichoderma longibrachiatum UENF-F476 boosting seedling growth of tomato and papaya. World J Microbiol Biotechnol 2021; 37:211. [PMID: 34729659 DOI: 10.1007/s11274-021-03179-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 10/26/2021] [Indexed: 11/28/2022]
Abstract
A plethora of bacteria-fungal interactions occur on the extended fungal hyphae network in soil. The mycosphere of saprophytic fungi can serve as a bacterial niche boosting their survival, dispersion, and activity. Such ecological concepts can be converted to bioproducts for sustainable agriculture. Accordingly, we tested the hypothesis that the well-characterised beneficial bacterium Serratia marcescens UENF-22GI can enhance plant growth-promoting properties when combined with Trichoderma longibrachiatum UENF-F476. The cultural and cell interactions demonstrated S. marcescens and T. longibrachiatum mutual compatibility. Bacteria cells were able to attach, forming aggregates to biofilms and migrating through the fungal hyphae network. Long-distance bacterial migration through growing hyphae was confirmed using a two-compartment Petri dishes assay. Fungal inoculation increased the bacteria survival rates into the vermicompost substrate over the experimental time. Also, in vitro indolic compound, phosphorus, and zinc solubilisation bacteria activities increased in the presence of the fungus. In line with the ecophysiological bacteria fitness, the bacterium-fungal combination boosted tomato and papaya plantlet growth when applied into the plant substrate under nursery conditions. Mutualistic interaction between mycosphere-colonizing bacterium S. marcescens UENF-22GI and the saprotrophic fungi T. longibrachiatum UENF-F467 increased the ecological fitness of the bacteria alongside with beneficial potential for plant growth. A proper combination and delivery of mutual compatible beneficial bacteria-fungal represent an open avenue for microbial-based products for the biological enrichment of plant substrates in agricultural systems.
Collapse
Affiliation(s)
- Régis Josué de Andrade Reis
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Alice Ferreira Alves
- Laboratório de Biologia Celular e Tecidual (LBCT), Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Pedro Henrique Dias Dos Santos
- Laboratório de Entomologia e Fitopatologia (LEF), Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Kamilla Pereira Aguiar
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Letícia Oliveira da Rocha
- Laboratório de Biologia Celular e Tecidual (LBCT), Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Silvaldo Felipe da Silveira
- Laboratório de Entomologia e Fitopatologia (LEF), Centro de Ciências e Tecnologias Agropecuárias (CCTA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Luciano Pasqualoto Canellas
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Fabio Lopes Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil. .,Laboratório de Biologia Celular e Tecidual (LBCT), Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, Brazil.
| |
Collapse
|
37
|
Yang N, Zhang C, Wang L, Li Y, Zhang W, Niu L, Zhang H, Wang L. Nitrogen cycling processes and the role of multi-trophic microbiota in dam-induced river-reservoir systems. WATER RESEARCH 2021; 206:117730. [PMID: 34619413 DOI: 10.1016/j.watres.2021.117730] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
The nitrogen (N) cycle is one of the most important nutrient cycles in river systems, and it plays an important role in maintaining biogeochemical balance and global climate stability. One of the main ways that humans have altered riverine ecosystems is through the construction of hydropower dams, which have major effects on biogeochemical cycles. Most previous studies examining the effects of damming on N cycling have focused on the whole budget or flux along rivers, and the role of river as N sources or sinks at the global or catchment scale. However, so far there is still lack of comprehensive and systematic summarize on N cycling and the controlling mechanisms in reservoirs affected by dam impoundment. In this review, we firstly summarize N cycling processes along the longitudinal riverine-transition-lacustrine gradient and the vertically stratified epilimnion-thermocline-hypolimnion gradient. Specifically, we highlight the direct and indirect roles of multi-trophic microbiota and their interactions in N cycling and discuss the main factors controlling these biotic processes. In addition, future research directions and challenges in incorporating multi-trophic levels in bioassessment, environmental flow design, as well as reservoir regulation and restoration are summarized. This review will aid future studies of N fluxes along dammed rivers and provide an essential reference for reservoir management to meet ecological needs.
Collapse
Affiliation(s)
- Nan Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| | - Chi Zhang
- College of Mechanics and Materials, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| | - Linqiong Wang
- College of Oceanography, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, P R China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| |
Collapse
|
38
|
Blagodatskaya E, Tarkka M, Knief C, Koller R, Peth S, Schmidt V, Spielvogel S, Uteau D, Weber M, Razavi BS. Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces. Front Microbiol 2021; 12:625697. [PMID: 34777265 PMCID: PMC8581545 DOI: 10.3389/fmicb.2021.625697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 09/01/2021] [Indexed: 12/30/2022] Open
Abstract
In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.
Collapse
Affiliation(s)
- Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- Agro-Technological Institute, RUDN University, Moscow, Russia
| | - Mika Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research Halle–Jena–Leipzig, Leipzig, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Stephan Peth
- Institute of Soil Science, University of Hannover, Hanover, Germany
| | | | - Sandra Spielvogel
- Department Soil Science, Institute for Plant Nutrition and Soil Science, Christian-Albrechts University Kiel, Kiel, Germany
| | - Daniel Uteau
- Department of Soil Science, Faculty of Organic Agricultural Sciences, University of Kassel, Kassel, Germany
| | | | - Bahar S. Razavi
- Department of Soil and Plant Microbiome, Institute of Phytopathology, Christian-Albrechts-University of Kiel, Kiel, Germany
| |
Collapse
|
39
|
Beugnon R, Du J, Cesarz S, Jurburg SD, Pang Z, Singavarapu B, Wubet T, Xue K, Wang Y, Eisenhauer N. Tree diversity and soil chemical properties drive the linkages between soil microbial community and ecosystem functioning. ISME COMMUNICATIONS 2021; 1:41. [PMID: 37938251 PMCID: PMC9723754 DOI: 10.1038/s43705-021-00040-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 05/26/2023]
Abstract
Microbial respiration is critical for soil carbon balance and ecosystem functioning. Previous studies suggest that plant diversity influences soil microbial communities and their respiration. Yet, the linkages between tree diversity, microbial biomass, microbial diversity, and microbial functioning have rarely been explored. In this study, we measured two microbial functions (microbial physiological potential, and microbial respiration), together with microbial biomass, microbial taxonomic and functional profiles, and soil chemical properties in a tree diversity experiment in South China, to disentangle how tree diversity affects microbial respiration through the modifications of the microbial community. Our analyses show a significant positive effect of tree diversity on microbial biomass (+25% from monocultures to 24-species plots), bacterial diversity (+12%), and physiological potential (+12%). In addition, microbial biomass and physiological potential, but not microbial diversity, were identified as the key drivers of microbial respiration. Although soil chemical properties strongly modulated soil microbial community, tree diversity increased soil microbial respiration by increasing microbial biomass rather than changing microbial taxonomic or functional diversity. Overall, our findings suggest a prevalence of microbial biomass over diversity in controlling soil carbon dynamics.
Collapse
Affiliation(s)
- Rémy Beugnon
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany.
- Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, Germany.
| | - Jianqing Du
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, Germany
| | - Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, Germany
| | - Zhe Pang
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Bala Singavarapu
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- UFZ-Helmholtz Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, Halle (Saale), Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor, Halle, Germany
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- UFZ-Helmholtz Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, Halle (Saale), Germany
| | - Kai Xue
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.
| | - Yanfen Wang
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, Germany
| |
Collapse
|
40
|
Shu L, He Z, Guan X, Yang X, Tian Y, Zhang S, Wu C, He Z, Yan Q, Wang C, Shi Y. A dormant amoeba species can selectively sense and predate on different soil bacteria. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13824] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Longfei Shu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology Sun Yat‐Sen University Guangzhou China
| | - Zhenzhen He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Xueqin Yang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Yuehui Tian
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Siyi Zhang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Chenyuan Wu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Zhili He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Qingyun Yan
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Cheng Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat‐sen University Guangzhou China
| | - Yijing Shi
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology Sun Yat‐Sen University Guangzhou China
- School of Environment Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment SCNU Environmental Research InstituteSouth China Normal University Guangzhou China
| |
Collapse
|
41
|
Clocchiatti A, Hannula SE, Hundscheid MPJ, Klein Gunnewiek PJA, de Boer W. Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings. Environ Microbiol 2021; 23:6056-6073. [PMID: 33973345 PMCID: PMC8596668 DOI: 10.1111/1462-2920.15563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 05/05/2021] [Indexed: 11/28/2022]
Abstract
Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose‐rich materials. Here, we examined if sawdust‐stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust‐amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following 13CO2‐pulse‐labelling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA‐SIP) and nucleic acids (DNA‐SIP). Sawdust‐stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α‐Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate‐consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root‐associated microbiomes.
Collapse
Affiliation(s)
- Anna Clocchiatti
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Soil Biology Group, Wageningen University, Wageningen, The Netherlands
| | - S Emilia Hannula
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Maria P J Hundscheid
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Soil Biology Group, Wageningen University, Wageningen, The Netherlands
| |
Collapse
|
42
|
Gaiero JR, Tosi M, Bent E, Boitt G, Khosla K, Turner BL, Richardson AE, Condron LM, Dunfield KE. Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand. FEMS Microbiol Ecol 2021; 97:6145523. [PMID: 33609120 DOI: 10.1093/femsec/fiab034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/18/2021] [Indexed: 01/04/2023] Open
Abstract
The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and alkaline (phoD) phosphomonoesterase genes and quantified specific genes and transcripts using real-time PCR. Soil bacterial diversity was greatest after 4000 years of ecosystem development and associated with an increased richness of phylotypes and a significant decline in previously dominant taxa (Firmicutes and Proteobacteria). Soil fungal communities transitioned from predominantly Basidiomycota to Ascomycota along the chronosequence and were most diverse in 290- to 392-year-old soils, coinciding with maximum tree basal area and organic P accumulation. The Bacteria:Fungi ratio decreased amid a competitive and interconnected soil community as determined by network analysis. Overall, soil microbial communities were associated with soil changes and declining P throughout pedogenesis and ecosystem succession. We identified an increased dependence on organic P mineralization, as found by the profiled acid phosphatase genes, soil acid phosphatase activity and function inference from predicted metagenomes (PICRUSt2).
Collapse
Affiliation(s)
- Jonathan R Gaiero
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Elizabeth Bent
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Gustavo Boitt
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Kamini Khosla
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Benjamin L Turner
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Republic of Panama
| | | | - Leo M Condron
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, Canterbury, New Zealand
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| |
Collapse
|
43
|
Lerner H, Öztürk B, Dohrmann AB, Thomas J, Marchal K, De Mot R, Dehaen W, Tebbe CC, Springael D. DNA-SIP and repeated isolation corroborate Variovorax as a key organism in maintaining the genetic memory for linuron biodegradation in an agricultural soil. FEMS Microbiol Ecol 2021; 97:6204700. [PMID: 33784375 DOI: 10.1093/femsec/fiab051] [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: 11/23/2020] [Accepted: 03/25/2021] [Indexed: 11/14/2022] Open
Abstract
The frequent exposure of agricultural soils to pesticides can lead to microbial adaptation, including the development of dedicated microbial populations that utilize the pesticide compound as a carbon and energy source. Soil from an agricultural field in Halen (Belgium) with a history of linuron exposure has been studied for its linuron-degrading bacterial populations at two time points over the past decade and Variovorax was appointed as a key linuron degrader. Like most studies on pesticide degradation, these studies relied on isolates that were retrieved through bias-prone enrichment procedures and therefore might not represent the in situ active pesticide-degrading populations. In this study, we revisited the Halen field and applied, in addition to enrichment-based isolation, DNA stable isotope probing (DNA-SIP), to identify in situ linuron-degrading bacteria in linuron-exposed soil microcosms. Linuron dissipation was unambiguously linked to Variovorax and its linuron catabolic genes and might involve the synergistic cooperation between two species. Additionally, two novel linuron-mineralizing Variovorax isolates were obtained with high 16S rRNA gene sequence similarity to strains isolated from the same field a decade earlier. The results confirm Variovorax as a prime in situ degrader of linuron in the studied agricultural field soil and corroborate the genus as key for maintaining the genetic memory of linuron degradation functionality in that field.
Collapse
Affiliation(s)
- Harry Lerner
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Başak Öztürk
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Anja B Dohrmann
- Thünen Institute of Biodiversity, Bundesallee 65, 388116 Braunschweig, Germany
| | - Joice Thomas
- Molecular Design and Synthesis, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics & Department of Information Technology, University of Ghent, iGent Toren, Technologiepark 126, B-9052 Ghent, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven, B-3001 Leuven, Belgium
| | - Wim Dehaen
- Molecular Design and Synthesis, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Bundesallee 65, 388116 Braunschweig, Germany
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| |
Collapse
|
44
|
Soil Organic Carbon Content Decreases in Both Surface and Subsoil Mineral Horizons by Simulated Future Increases in Labile Carbon Inputs in a Temperate Coniferous Forest. Ecosystems 2021. [DOI: 10.1007/s10021-021-00632-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
45
|
Wang C, Xiao R, Guo Y, Wang Q, Cui Y, Xiu Y, Ma Z, Zhang M. Changes in soil microbial community composition during Phragmites australis straw decomposition in salt marshes with freshwater pumping. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 762:143996. [PMID: 33360338 DOI: 10.1016/j.scitotenv.2020.143996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 11/04/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
The dynamic changes of soil microorganisms after Phragmites australis straw addition in the incubation tubes were analyzed by phospholipid fatty acid stable isotope probing (PLFA-SIP). After comparing soils from different freshwater pumping areas in the Yellow River Estuary (10-year pumping area, 15-year pumping area and natural salt marsh without pumping), the results showed that the total PLFA contents significantly increased by 59.99%-146.93% after the addition of straw to surface soils (0-10 cm) in the pumping areas, whereas the changes in deeper soils (10-20 cm) were not significant. In particular, the PLFA results showed that bacteria and fungi were significantly increased after 10 days with straw addition. Straw treatment also improved the ratio of fungi to bacteria (F:B) in the surface soils of all sampling sites. The soil microorganisms directly absorbed straw-derived 13C, where Gram-negative bacteria (GN) were found to have the highest PLFA-13C values during the 40-day decomposition process. Soil characteristics can significantly affect microbial community composition. Accordingly, soil organic carbon (SOC) was found to be significantly positively related to bacterial, fungal and other microbial biomasses, while moisture, electric conductivity (EC) and soil aggregate composition were important factors of influence on the microbial community. The findings indicated that both fungi and bacteria were essential microbial communities in straw decomposition, the significant increase of fungi biomass and the absorption of straw-derived 13C by bacteria were the main changes of microbial community. Long-term freshwater pumping can promote straw decomposition by increasing microbial biomass and changing microbial community composition.
Collapse
Affiliation(s)
- Chen Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China; School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Rong Xiao
- College of Environment and Resources, Fuzhou University, Fuzhou 350116, China.
| | - Yutong Guo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Qian Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yuan Cui
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yujiao Xiu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Ziwen Ma
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Mingxiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China.
| |
Collapse
|
46
|
Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil. mBio 2021; 12:mBio.03099-20. [PMID: 33402535 PMCID: PMC8545098 DOI: 10.1128/mbio.03099-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing 13C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most 13C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed 13C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and 13C labeling (i.e., partial labeling or labeling at later stages). Major 13C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.
Collapse
|
47
|
Hannula S, Morriën E, van der Putten W, de Boer W. Rhizosphere fungi actively assimilating plant-derived carbon in a grassland soil. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100988] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
48
|
Zhou Y, Zhang X, Yao Q, Zhu H. Both Soil Bacteria and Soil Chemical Property Affected the Micropredator Myxobacterial Community: Evidence from Natural Forest Soil and Greenhouse Rhizosphere Soil. Microorganisms 2020; 8:E1387. [PMID: 32927762 PMCID: PMC7563646 DOI: 10.3390/microorganisms8091387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 01/19/2023] Open
Abstract
Myxobacteria are abundant micropredators in soil, and are social bacteria with multicellular behavior and producers of versatile secondary metabolites. The interaction between predator and prey populations is an important component in the soil microbial food web, and this is expected to shape the composition and dynamics of microbial communities. Here we hypothesize the regulation of bacterial abundance and community composition on soil myxobacterial community. Field investigation indicated that the relative abundance of Myxococcales in subtropical and tropical forest soil from South China was 1.49-4.74% of all the 16S rRNA gene sequences, and myxobacterial community composition differed between subtropical and tropical forest. The canonical correspondence analysis and variation partitioning analysis indicated that biotic factor (bacterial community composition) showed slightly stronger explanation for variation of myxobacteria than soil properties (soil pH and soil organic matter). Based on the rhizosphere bacterial network, the greenhouse mesocosm experiment showed that most of the myxobacterial links were with Gram-negative bacteria, except that some nodes from Haliangiacea and Polyangiaceae interacted with actinomycetes and actinomycetes-like Gram-positive bacteria. We inferred that myxobacteria preferential predation on specific bacterial taxa may explain the influence of bacteria on myxobacterial community. Further study confirming the biological process of myxobacterial predation in situ is necessary to advance the understanding of the ecological role of predation behavior in the microbial world.
Collapse
Affiliation(s)
- Yang Zhou
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (Y.Z.); (X.Z.)
| | - Xianjiao Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (Y.Z.); (X.Z.)
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass Science, Guangzhou 510642, China
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (Y.Z.); (X.Z.)
| |
Collapse
|
49
|
Lerner H, Öztürk B, Dohrmann AB, Thomas J, Marchal K, De Mot R, Dehaen W, Tebbe CC, Springael D. Culture-Independent Analysis of Linuron-Mineralizing Microbiota and Functions in on-Farm Biopurification Systems via DNA-Stable Isotope Probing: Comparison with Enrichment Culture. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:9387-9397. [PMID: 32569463 DOI: 10.1021/acs.est.0c02124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Our understanding of the microorganisms involved in in situ biodegradation of xenobiotics, like pesticides, in natural and engineered environments is poor. On-farm biopurification systems (BPSs) treat farm-produced pesticide-contaminated wastewater to reduce surface water pollution. BPSs are a labor and cost-efficient technology but are still mainly operated as black box systems. We used DNA-stable isotope probing (DNA-SIP) and classical enrichment to be informed about the organisms responsible for in situ degradation of the phenylurea herbicide linuron in a BPS matrix. DNA-SIP identified Ramlibacter, Variovorax, and an unknown Comamonadaceae genus as the dominant linuron assimilators. While linuron-degrading Variovorax strains have been isolated repeatedly, Ramlibacter has never been associated before with linuron degradation. Genes and mobile genetic elements (MGEs) previously linked to linuron catabolism were enriched in the heavy DNA-SIP fractions, suggesting their involvement in in situ linuron assimilation. BPS material free cultivation of linuron degraders from the same BPS matrix resulted in a community dominated by Variovorax, while Ramlibacter was not observed. Our study provides evidence for the role of Variovorax in in situ linuron biodegradation in a BPS, alongside other organisms like Ramlibacter, and further shows that cultivation results in a biased representation of the in situ linuron-assimilating bacterial populations.
Collapse
Affiliation(s)
- Harry Lerner
- Division of Soil and Water Management, KU Leuven, B-3001 Heverlee-Leuven, Belgium
| | - Başak Öztürk
- Division of Soil and Water Management, KU Leuven, B-3001 Heverlee-Leuven, Belgium
| | - Anja B Dohrmann
- Thünen Institut für Biodiversität, 38116 Braunschweig, Germany
| | - Joice Thomas
- Molecular Design and Synthesis, KU Leuven, B-3001 Heverlee-Leuven, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9000 Gent, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven, B-3001 Heverlee-Leuven, Belgium
| | - Wim Dehaen
- Molecular Design and Synthesis, KU Leuven, B-3001 Heverlee-Leuven, Belgium
| | | | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, B-3001 Heverlee-Leuven, Belgium
| |
Collapse
|
50
|
Zhou Y, Coventry DR, Gupta VVSR, Fuentes D, Merchant A, Kaiser BN, Li J, Wei Y, Liu H, Wang Y, Gan S, Denton MD. The preceding root system drives the composition and function of the rhizosphere microbiome. Genome Biol 2020; 21:89. [PMID: 32252812 PMCID: PMC7137527 DOI: 10.1186/s13059-020-01999-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The soil environment is responsible for sustaining most terrestrial plant life, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere, and how it responds to agricultural management such as crop rotations and soil tillage, is vital for improving global food production. RESULTS This study establishes an in-depth soil microbial gene catalogue based on the living-decaying rhizosphere niches in a cropping soil. The detritusphere microbiome regulates the composition and function of the rhizosphere microbiome to a greater extent than plant type: rhizosphere microbiomes of wheat and chickpea were homogenous (65-87% similarity) in the presence of decaying root (DR) systems but were heterogeneous (3-24% similarity) where DR was disrupted by tillage. When the microbiomes of the rhizosphere and the detritusphere interact in the presence of DR, there is significant degradation of plant root exudates by the rhizosphere microbiome, and genes associated with membrane transporters, carbohydrate and amino acid metabolism are enriched. CONCLUSIONS The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the detritusphere microbiome in determining the metagenome of developing root systems. Modifications in root microbial function through soil management can ultimately govern plant health, productivity and food security.
Collapse
Affiliation(s)
- Yi Zhou
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064 Australia
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA 5064 Australia
| | - David R. Coventry
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064 Australia
| | | | - David Fuentes
- School of Life and Environmental Sciences, University of Sydney, Brownlow Hill, NSW 2570 Australia
| | - Andrew Merchant
- School of Life and Environmental Sciences, University of Sydney, Brownlow Hill, NSW 2570 Australia
| | - Brent N. Kaiser
- School of Life and Environmental Sciences, University of Sydney, Brownlow Hill, NSW 2570 Australia
| | - Jishun Li
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA 5064 Australia
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong, 250013 China
| | - Yanli Wei
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA 5064 Australia
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong, 250013 China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen, 518083 Guangdong China
| | - Yayu Wang
- BGI-Shenzhen, Shenzhen, 518083 Guangdong China
| | - Shuheng Gan
- BGI-Shenzhen, Shenzhen, 518083 Guangdong China
| | - Matthew D. Denton
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064 Australia
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, The University of Adelaide, Glen Osmond, SA 5064 Australia
| |
Collapse
|