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Yang L, Wang C, He X, Liang H, Wu Q, Sun X, Liu M, Shen P. Multi-year crop rotation and quicklime application promote stable peanut yield and high nutrient-use efficiency by regulating soil nutrient availability and bacterial/fungal community. Front Microbiol 2024; 15:1367184. [PMID: 38827150 PMCID: PMC11140132 DOI: 10.3389/fmicb.2024.1367184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/06/2024] [Indexed: 06/04/2024] Open
Abstract
Diversifying cultivation management, including different crop rotation patterns and soil amendment, are effective strategies for alleviating the obstacles of continuous cropping in peanut (Arachis hypogaea L.). However, the peanut yield enhancement effect and temporal changes in soil chemical properties and microbial activities in response to differential multi-year crop rotation patterns and soil amendment remain unclear. In the present study, a multi-year localization experiment with the consecutive application of five different cultivation managements (including rotation with different crops under the presence or absence of external quicklime as soil amendment) was conducted to investigate the dynamic changes in peanut nutrient uptake and yield status, soil chemical property, microbial community composition and function. Peanut continuous cropping led to a reduction in peanut yield, while green manure-peanut rotation and wheat-maize-peanut rotation increased peanut yield by 40.59 and 81.95%, respectively. A combination of quicklime application increased yield by a further 28.76 and 24.34%. Alterations in cultivation management also strongly affected the soil pH, nutrient content, and composition and function of the microbial community. The fungal community was more sensitive than the bacterial community to cultivation pattern shift. Variation in bacterial community was mainly attributed to soil organic carbon, pH and calcium content, while variation in fungal community was more closely related to soil phosphorus content. Wheat-maize-peanut rotation combined with quicklime application effectively modifies the soil acidification environment, improves the soil fertility, reshapes the composition of beneficial and harmful microbial communities, thereby improving soil health, promoting peanut development, and alleviating peanut continuous cropping obstacles. We concluded that wheat-maize-peanut rotation in combination with quicklime application was the effective practice to improve the soil fertility and change the composition of potentially beneficial and pathogenic microbial communities in the soil, which is strongly beneficial for building a healthy soil micro-ecology, promoting the growth and development of peanut, and reducing the harm caused by continuous cropping obstacles to peanut.
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Affiliation(s)
- Liyu Yang
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Caibin Wang
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Xinhua He
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Haiyan Liang
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Qi Wu
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Xuewu Sun
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Miao Liu
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Pu Shen
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
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Liu S, Huang J, He W, Shi L, Zhang W, Li E, Hu J, Zhang C, Pang H. Effects of microplastics on microbial community structure and wheatgrass traits in Pb-contaminated riparian sediments under flood-drainage-planting conditions. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134283. [PMID: 38613956 DOI: 10.1016/j.jhazmat.2024.134283] [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: 02/05/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
The coexistence of microplastics (MPs) and heavy metals in sediments has caused a potential threat to sediment biota. However, differences in the effects of MPs and heavy metals on microbes and plants in sediments under different sediment conditions remain unclear. Hence, we investigated the influence of polyethylene (PE) and polylactic acid (PLA) MPs on microbial community structure, Pb bioavailability, and wheatgrass traits under sequential incubation of sediments (i.e., flood, drainage, and planting stages). Results showed that the sediment enzyme activities presented a dose-dependent effect of MPs. Besides, 10 % PLA MPs significantly increased the F1 fractions in three stages by 11.13 %, 30.10 %, and 17.26 %, respectively, thus resulting in higher Pb mobility and biotoxicity. MPs altered sediment bacterial composition and structures, and bacterial community differences were evident in different incubation stages. Moreover, the co-exposure of PLA MPs and Pb significantly decreased the shoot length and total biomass of wheatgrass and correspondingly activated the antioxidant enzyme activity. Further correlation analysis demonstrated that community structure induced by MPs was mainly driven by sediment enzyme activity. This study contributes to elucidating the combined effects of MPs and heavy metals on sediment ecosystems under different sediment conditions.
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Affiliation(s)
- Si Liu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Jinhui Huang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Wenjuan He
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Lixiu Shi
- College of Hydraulic and Environmental Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Wei Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Enjie Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Jinying Hu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Chenyu Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Haoliang Pang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
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Guo P, Du H, Zhao W, Xiong B, Wang M, He M, Flemetakis E, Hänsch R, Ma M, Rennenberg H, Wang D. Selenium- and chitosan-modified biochars reduce methylmercury contents in rice seeds with recruiting Bacillus to inhibit methylmercury production. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133236. [PMID: 38141298 DOI: 10.1016/j.jhazmat.2023.133236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/13/2023] [Accepted: 12/10/2023] [Indexed: 12/25/2023]
Abstract
Biochar could reshape microbial communities, thereby altering methylmercury (MeHg) concentrations in rice rhizosphere and seeds. However, it remains unclear whether and how biochar amendment perturbs microbe-mediated MeHg production in mercury (Hg) contaminated paddy soil. Here, we used pinecone-derived biochar and its six modified biochars to reveal the disturbance. Results showed that selenium- and chitosan-modified biochar significantly reduced MeHg concentrations in the rhizosphere by 85.83% and 63.90%, thereby decreasing MeHg contents in seeds by 86.37% and 75.50%. The two modified bicohars increased the abundance of putative Hg-resistant microorganisms Bacillus, the dominant microbe in rhizosphere. These reductions about MeHg could be facilitated by biochar sensitive microbes such as Oxalobacteraceae and Subgroup_7. Pinecone-derived biochar increased MeHg concentration in rhizosphere but unimpacted MeHg content in seeds was observed. This biochar decreased the abundance in Bacillus but enhanced in putative Hg methylator Desulfovibrio. The increasing MeHg concentration in rhizosphere could be improved by biochar sensitive microbes such as Saccharimonadales and Clostridia. Network analysis showed that Saccharimonadales and Clostridia were the most prominent keystone taxa in rhizosphere, and the three biochars manipulated abundances of the microbes related to MeHg production in rhizosphere by those biochar sensitive microbes. Therefore, selenium- and chitosan-modified biochar could reduce soil MeHg production by these microorganisms, and is helpful in controlling MeHg contamination in rice.
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Affiliation(s)
- Pan Guo
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Hongxia Du
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Wancang Zhao
- Chongqing Key Laboratory of Karst Environment, School of Geographical Sciences, Southwest University, Chongqing 400715, PR China
| | - Bingcai Xiong
- Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Mingxing Wang
- Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Chongqing 400715, PR China
| | - Mingyan He
- Chongqing Ecological Environment Monitoring Center, Chongqing 401147, PR China
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Robert Hänsch
- Institute for Plant Biology, Technische Universität Braunschweig, Humboldtstraße 1, D-38106, Braunschweig, Germany
| | - Ming Ma
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China; Chongqing Key Laboratory of Bio-resource for Bioenergy, College of Resources and Environment, Southwest University, Chongqing 400715, PR China.
| | - Heinz Rennenberg
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Dingyong Wang
- Chongqing Key Laboratory of Agricultural Resources and Environment, College of Resources and Environment, Chongqing 400715, PR China
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Li X, Bei Q, Rabiei Nematabad M, Peng J, Liesack W. Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil. MICROBIOME 2024; 12:39. [PMID: 38409166 PMCID: PMC10895765 DOI: 10.1186/s40168-023-01739-z] [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: 09/05/2023] [Accepted: 12/18/2023] [Indexed: 02/28/2024]
Abstract
BACKGROUND The final step in the anaerobic decomposition of biopolymers is methanogenesis. Rice field soils are a major anthropogenic source of methane, with straw commonly used as a fertilizer in rice farming. Here, we aimed to decipher the structural and functional responses of the methanogenic community to rice straw addition during an extended anoxic incubation (120 days) of Philippine paddy soil. The research combined process measurements, quantitative real-time PCR and RT-PCR of particular biomarkers (16S rRNA, mcrA), and meta-omics (environmental genomics and transcriptomics). RESULTS The analysis methods collectively revealed two major bacterial and methanogenic activity phases: early (days 7 to 21) and late (days 28 to 60) community responses, separated by a significant transient decline in microbial gene and transcript abundances and CH4 production rate. The two methanogenic activity phases corresponded to the greatest rRNA and mRNA abundances of the Methanosarcinaceae but differed in the methanogenic pathways expressed. While three genetically distinct Methanosarcina populations contributed to acetoclastic methanogenesis during the early activity phase, the late activity phase was defined by methylotrophic methanogenesis performed by a single Methanosarcina genomospecies. Closely related to Methanosarcina sp. MSH10X1, mapping of environmental transcripts onto metagenome-assembled genomes (MAGs) and population-specific reference genomes revealed this genomospecies as the key player in acetoclastic and methylotrophic methanogenesis. The anaerobic food web was driven by a complex bacterial community, with Geobacteraceae and Peptococcaceae being putative candidates for a functional interplay with Methanosarcina. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while the acetoclastic activity of Methanotrichaceae members was detectable only during the very late community response. CONCLUSIONS The predominant but time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies represents a novel finding that expands our hitherto knowledge of the methanogenic pathways being highly expressed in paddy soils. Video Abstract.
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Affiliation(s)
- Xin Li
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
- Present address: Institute of Agricultural and Nutritional Sciences, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Strasse 5, Halle (Saale), Germany
| | - Qicheng Bei
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
- Present address: Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Strasse 4, Halle (Saale), Germany
| | - Mehrdad Rabiei Nematabad
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany
| | - Jingjing Peng
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
| | - Werner Liesack
- Research group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043, Marburg, Germany.
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Wang M, Qi X, Shi Y, Zhao J, Ahmad S, Akhtar K, Chen B, Lian T, He B, Wen R. Sugarcane straw returning is an approaching technique for the improvement of rhizosphere soil functionality, microbial community, and yield of different sugarcane cultivars. Front Microbiol 2023; 14:1133973. [PMID: 36998394 PMCID: PMC10043380 DOI: 10.3389/fmicb.2023.1133973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/24/2023] [Indexed: 03/15/2023] Open
Abstract
Sugarcane straw returned to the field has rapidly increased due to the bane on straw burning in China. Straw returning of new sugarcane cultivars has been practiced in the fields. Still, its response has not been explored on soil functionality, microbial community and yield of different sugarcane cultivars. Therefore, a comparison was made between an old sugarcane cultivar ROC22 and a new sugarcane cultivar Zhongzhe9 (Z9). The experimental treatments were: without (R, Z), with straw of the same cultivar (RR, ZZ), and with straw of different cultivars (RZ, ZR). Straw returning improved the contents of soil total nitrogen (TN by 73.21%), nitrate nitrogen (NO3—N by 119.61%), soil organic carbon (SOC by 20.16%), and available potassium (AK by 90.65%) at the jointing stage and were not significant at the seedling stage. The contents of NO3—N was 31.94 and 29.58%, available phosphorus (AP 53.21 and 27.19%), and available potassium (AK 42.43 and 11.92%) in RR and ZZ were more than in RZ and ZR. Straw returning with the same cultivar (RR, ZZ) significantly increased the richness and diversity of the rhizosphere microbial community. The microbial diversity of cultivar Z9 (treatment Z) was greater than that of cultivar ROC22 (Treatment R). In the rhizosphere, the relative abundance of beneficial microorganisms Gemmatimonadaceae, Trechispora, Streptomyces, Chaetomium, etc., increased after the straw returned. Sugarcane straw enhanced the activity of Pseudomonas and Aspergillus and thus increased the yield of sugarcane., The richness and diversity of the rhizosphere microbial community of Z9 increased at maturity. In ROC22, bacterial diversity increased, and fungal diversity decreased. These findings collectively suggested that the impact of Z9 straw returning was more beneficial than ROC22 on the activity of rhizosphere microorganism’s soil functionality and sugarcane production.
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Affiliation(s)
- Mengrong Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Ministry and Province Co-sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Xiaohang Qi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Ministry and Province Co-sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Yujie Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Ministry and Province Co-sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Junyang Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Ministry and Province Co-sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Shakeel Ahmad
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Ministry and Province Co-sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Kashif Akhtar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Ministry and Province Co-sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Ministry and Province Co-sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, China
| | - Tengxiang Lian
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Bing He
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, China
- *Correspondence: Bing He,
| | - Ronghui Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Ministry and Province Co-sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China
- Ronghui Wen,
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Zhang S, Li X, Chen K, Shi J, Wang Y, Luo P, Yang J, Wang Y, Han X. Long-term fertilization altered microbial community structure in an aeolian sandy soil in northeast China. Front Microbiol 2022; 13:979759. [PMID: 36160213 PMCID: PMC9490088 DOI: 10.3389/fmicb.2022.979759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022] Open
Abstract
Soil microorganisms play crucial roles in nutrient cycling and determining soil quality and fertility; thus, they are important for agricultural production. However, the impacts of long-term fertilization on soil microbial community remain ambiguous due to inconsistent results from different studies. The objective of this study was to characterize changes in bacterial and fungal diversity and community structures after 12 years of different fertilization in aeolian sandy soil by analyzing 16S rRNA and ITS rRNA gene sequences and the soil properties to discover the driving factors. Eight different fertilizer treatments have been set up since 2009: no fertilizer (CK), chemical N fertilizer (N), chemical N and P fertilizer (NP), chemical N, P and K fertilizer (NPK), pig manure only (M), pig manure plus chemical N fertilizer (MN), pig manure plus chemical N and P fertilizer (MNP), pig manure plus chemical N, P, and K fertilizer (MNPK). The results indicated that the long-term application of chemical fertilizer reduced soil pH, whereas the addition of pig manure alleviated a decrease in soil pH value. Chemical fertilizer plus pig manure significantly improved soil available nutrients and soil organic carbon. Long-term MNPK fertilization resulted in changes in bacterial diversity due to effects on specific bacterial species; by contrast, all fertilization treatments resulted in changes in fungal diversity due to changes in soil properties. Principal component analysis indicated that fertilization had a significant effect on soil microbial community structure, and the effect of chemical fertilizer combined with pig manure was greater than that of chemical fertilizer alone. Soil available phosphorus, total phosphorus, and pH were the most important factors that influenced bacterial taxa, whereas soil pH, total phosphorus, organic carbon, ammonium nitrogen and nitrate nitrogen were the most important factors influencing fungal taxa after 12 years of fertilization in aeolian sandy soil.
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Affiliation(s)
- Shiyu Zhang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
| | - Xue Li
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
| | - Kun Chen
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
| | - Junmei Shi
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
| | - Yan Wang
- Department of Foreign Languages, Shenyang Agricultural University, Shenyang, China
| | - Peiyu Luo
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
| | - Jinfeng Yang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
| | - Yue Wang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
- *Correspondence: Yue Wang,
| | - Xiaori Han
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
- Xiaori Han,
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7
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Hall SJ, Huang W, Napieralski SA, Roden E. Shared Microbial Taxa Respond Predictably to Cyclic Time-Varying Oxygen Limitation in Two Disparate Soils. Front Microbiol 2022; 13:866828. [PMID: 35722278 PMCID: PMC9203030 DOI: 10.3389/fmicb.2022.866828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/16/2022] [Indexed: 11/27/2022] Open
Abstract
Periodic oxygen (O2) limitation in humid terrestrial soils likely influences microbial composition, but whether communities share similar responses in disparate environments remains unclear. To test if specific microbial taxa share consistent responses to anoxia in radically different soils, we incubated a rainforest Oxisol and cropland Mollisol under cyclic, time-varying anoxic/oxic cycles in the laboratory. Both soils are known to experience anoxic periods of days to weeks under field conditions; our incubation treatments consisted of anoxic periods of 0, 2, 4, 8, or 12 d followed by 4 d of oxic conditions, repeated for a total of 384 d. Taxa measured by 16S rRNA gene sequences after 48 d and 384 d of experimental treatments varied strongly with increasing anoxic period duration, and responses to anoxia often differed between soils at multiple taxonomic levels. Only 19% of the 30,356 operational taxonomic units (OTUs) occurred in both soils, and most OTUs did not respond consistently to O2 treatments. However, the OTUs present in both soils were disproportionally abundant, comprising 50% of sequences, and they often had a similar response to anoxic period duration in both soils (p < 0.0001). Overall, 67 OTUs, 36 families, 15 orders, 10 classes, and two phyla had significant and directionally consistent (positive or negative) responses to anoxic period duration in both soils. Prominent OTUs and taxonomic groups increasing with anoxic period duration in both soils included actinomycetes (Micromonosporaceae), numerous Ruminococcaceae, possible metal reducers (Anaeromyxobacter) or oxidizers (Candidatus Koribacter), methanogens (Methanomicrobia), and methanotrophs (Methylocystaceae). OTUs decreasing with anoxic duration in both soils included nitrifiers (Nitrospira) and ubiquitous unidentified Bradyrhizobiaceae and Micromonosporaceae. Even within the same genus, different OTUs occasionally showed strong positive or negative responses to anoxic duration (e.g., Dactylosporangium in the Actinobacteria), highlighting a potential for adaptation or niche partitioning in variable-O2 environments. Overall, brief anoxic periods impacted the abundance of certain microbial taxa in predictable ways, suggesting that microbial community data may partially reflect and integrate spatiotemporal differences in O2 availability within and among soils.
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Affiliation(s)
- Steven J. Hall
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
- *Correspondence: Steven J. Hall,
| | - Wenjuan Huang
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | | | - Eric Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
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8
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Yurgel SN, Nadeem M, Cheema M. Microbial Consortium Associated with Crustacean Shells Composting. Microorganisms 2022; 10:1033. [PMID: 35630475 PMCID: PMC9145653 DOI: 10.3390/microorganisms10051033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
Soil microbes play an essential role in the biodegradation of crustacean shells, which is the process of sustainable bioconversion to chitin derivatives ultimately resulting in the promotion of plant growth properties. While a number of microorganisms with chitinolytic properties have been characterized, little is known about the microbial taxa that participate in this process either by active chitin degradation or by facilitation of this activity through nutritional cooperation and composting with the chitinolytic microorganisms. In this study, we evaluated the transformation of the soil microbiome triggered by close approximation to the green crab shell surface. Our data indicate that the microbial community associated with green crab shell matter undergoes significant specialized changes, which was reflected in a decreased fungal and bacterial Shannon diversity and evenness and in a dramatic alteration in the community composition. The relative abundance of several bacterial and fungal genera including bacteria Flavobacterium, Clostridium, Pseudomonas, and Sanguibacter and fungi Mortierella, Mycochlamys, and Talaromyces were increased with approximation to the shell surface. Association with the shell triggered significant changes in microbial cooperation that incorporate microorganisms that were previously reported to be involved in chitin degradation as well as ones with no reported chitinolytic activity. Our study indicates that the biodegradation of crab shells in soil incorporates a consortium of microorganisms that might provide a more efficient way for bioconversion.
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Affiliation(s)
- Svetlana N. Yurgel
- USDA-ARS, Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA
| | - Muhammad Nadeem
- School of Science and the Environment, Grenfell Campus, Memorial University of Newfoundland and Labrador, Corner Brook, NL A2H 5G4, Canada; (M.N.); (M.C.)
| | - Mumtaz Cheema
- School of Science and the Environment, Grenfell Campus, Memorial University of Newfoundland and Labrador, Corner Brook, NL A2H 5G4, Canada; (M.N.); (M.C.)
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9
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Bai YC, Li BX, Xu CY, Raza M, Wang Q, Wang QZ, Fu YN, Hu JY, Imoulan A, Hussain M, Xu YJ. Intercropping Walnut and Tea: Effects on Soil Nutrients, Enzyme Activity, and Microbial Communities. Front Microbiol 2022; 13:852342. [PMID: 35369467 PMCID: PMC8971985 DOI: 10.3389/fmicb.2022.852342] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/08/2022] [Indexed: 11/21/2022] Open
Abstract
The practice of intercropping, which involves growing more than one crop simultaneously during the same growing season, is becoming more important for increasing soil quality, land-use efficiency, and subsequently crop productivity. The present study examined changes in soil physicochemical properties, enzymatic activity, and microbial community composition when walnut (Juglans spp.) was intercropped with tea (Camellia sinensis L.) plants in a forest and compared with a walnut and tea monocropping system. The results showed that walnut-tea intercropping improved the soil nutrient profile and enzymatic activity. The soil available nitrogen (AN), available phosphorus (AP), available potassium (AK), organic matter (OM) content, and sucrase activity were significantly boosted in intercropped walnut and tea than in monocropping forests. The interaction between crops further increased bacterial and fungal diversity when compared to monoculture tea forests. Proteobacteria, Bacteroidetes, Firmicutes, Chlamydiae, Rozellomycota, and Zoopagomycota were found in greater abundance in an intercropping pattern than in monoculture walnut and tea forest plantations. The walnut-tea intercropping system also markedly impacted the abundance of several bacterial and fungal operational taxonomic units (OTUs), which were previously shown to support nutrient cycling, prevent diseases, and ameliorate abiotic stress. The results of this study suggest that intercropping walnut with tea increased host fitness and growth by positively influencing soil microbial populations.
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Affiliation(s)
- Yong-Chao Bai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bao-Xin Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | | | - Mubashar Raza
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Qi-Zhu Wang
- Center for Walnut Technology of Baokang County, Xiangyang, China
| | - Ya-Nan Fu
- Center for Walnut Technology of Baokang County, Xiangyang, China
| | - Jian-Yang Hu
- State Key Laboratory of the Discovery and Development of Novel Pesticides, Shenyang Sinochem Agrochemicals R&D Co., Ltd., Shenyang, China
| | - Abdessamad Imoulan
- Department of Biology, Faculty of Science and Technics of Errachidia, Mouly Ismail University, Meknes, Morocco
| | - Muzammil Hussain
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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10
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Liu X, Shi Y, Kong L, Tong L, Cao H, Zhou H, Lv Y. Long-Term Application of Bio-Compost Increased Soil Microbial Community Diversity and Altered Its Composition and Network. Microorganisms 2022; 10:microorganisms10020462. [PMID: 35208916 PMCID: PMC8878586 DOI: 10.3390/microorganisms10020462] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/08/2022] [Indexed: 01/10/2023] Open
Abstract
The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of soil and community composition. High dosages of bio-compost significantly increased the bacterial and fungal richness. The compositions of bacterial and fungal communities were significantly altered by bio-compost addition. Bio-compost addition enriched the relative abundance of beneficial microorganisms (such as Sphingomonas, Acidibacter, Nocardioides, etc.) and reduced the relative abundance of harmful microorganisms (such as Stachybotrys and Aspergillus). Electrical conductivity, soil organic matter and total phosphorus were the key factors in shaping soil microbial community composition. The bacterial network was more complex than fungal network, and bacteria were more sensitive to changes in environmental factors than fungi. Positive interactions dominated both the bacterial and fungal networks, with stronger positive interactions found in the bacterial network. Functional prediction suggested that bio-composts altered the soil bacterial-community metabolic function with respect to carbon, nitrogen and phosphorus cycles and fungal community trophic modes. In conclusion, suitable bio-compost addition is beneficial to the improvement of soil health and crop quality and therefore the sustainability of agriculture.
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Affiliation(s)
- Xiayan Liu
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China;
| | - Lingyu Kong
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
| | - Lihong Tong
- State Key Laboratory of Hydroscience and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing 100084, China;
| | - Haoxuan Cao
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
| | - Hu Zhou
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
- Correspondence: (H.Z.); (Y.L.); Tel.: +86-010-62731890 (H.Z.); +86-010-62731431 (Y.L.)
| | - Yizhong Lv
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
- Correspondence: (H.Z.); (Y.L.); Tel.: +86-010-62731890 (H.Z.); +86-010-62731431 (Y.L.)
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11
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Hester ER, Vaksmaa A, Valè G, Monaco S, Jetten MSM, Lüke C. Effect of water management on microbial diversity and composition in an Italian rice field system. FEMS Microbiol Ecol 2022; 98:6529233. [PMID: 35170720 PMCID: PMC8924702 DOI: 10.1093/femsec/fiac018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/26/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
Traditional rice cultivation consumes up to 2500 L of water per kg yield and new strategies such as the ‘Alternate Wetting and Drying’ (AWD) might be promising water-saving alternatives. However, they might have large impacts on the soil microbiology. In this study, we compared the bacterial and archaeal communities in experimental field plots, cultivated under continuously flooding (CF) and AWD management, by high-throughput sequencing of the 16S rRNA gene. We analysed alpha and beta diversity in bulk soil and on plant roots, in plots cultivated with two different rice cultivars. The strongest difference was found between soil and root communities. Beside others, the anaerobic methanotroph Methanoperedens was abundant in soil, however, we detected a considerable number of ANME-2a-2b on plant roots. Furthermore, root communities were significantly affected by the water management: Differential abundance analysis revealed the enrichment of aerobic and potentially plant-growth-promoting bacteria under AWD treatment, such as Sphingomonadaceae and Rhizobiaceae (both Alphaproteobacteria), and Bacteroidetes families. Microorganisms with an overall anaerobic lifestyle, such as various Delta- and Epsilonproteobacteria, and Firmicutes were depleted. Our study indicates that the bulk soil communities seem overall well adapted and more resistant to changes in the water treatment, whereas the root microbiota seems more vulnerable.
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Affiliation(s)
- Eric R Hester
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Giampiero Valè
- CREA - Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy.,DiSIT-Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Piazza San Eusebio 5, I-13100 Vercelli, Italy
| | - Stefano Monaco
- CREA - Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
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12
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Haris M, Hamid Y, Wang L, Wang M, Yashir N, Su F, Saleem A, Guo J, Li Y. Cd diminution through microbial mediated degraded lignocellulose maize straw: Batch adsorption and bioavailability trails. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 302:114042. [PMID: 34872180 DOI: 10.1016/j.jenvman.2021.114042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/16/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Lignocellulose degraded maize straw (LMS) was prepared with the interaction of soil-indigenous microorganisms and further deployed to attenuate the Cd contamination in polluted soil. The Lignocellulose degrading ratio was determined and results revealed the significant degradation of cellulose, hemicellulose and lignin by 33.03, 26.7 and 15.97% respectively as compared to pristine maize straw (PS). Moreover, LMS was also categorized through FE-SEM, FTIR, BET analysis, elemental analysis and XPS technique and the analytical results indicated that lignocellulose structure in maize straw was successfully degraded and was involved in metal-ion complexation. Batch sorption trials revealed that Cd2+ sorption onto LMS was explained well by Langmuir isotherm and pseudo-second-order kinetic model. The LMS showed maximum adsorption capacities (9.84 mg g-1) for Cd2+ as compared to PS (3.30 mg g-1). Moreover, the soil incubation trials (60 days) depicted the availability of Cd decreased by 11.03 and 34.7% with PS and LMS application respectively. The addition of LMS significantly decreased the exchangeable fractions of Cd and ensued an increase in organic matter and Fe-Mn oxides bound fractions. This work clarified the LMS as a promising amendment for effective remediation of Cd-contaminated matrices.
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Affiliation(s)
- Muhammad Haris
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Yasir Hamid
- Ministry of Education (MOE) Key Lab of Environ. Remediation and Ecol. Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, PR China
| | - Lei Wang
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Min Wang
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Nauman Yashir
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Fang Su
- School of Economics and Management, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Atif Saleem
- Frontiers Science Center for Flexible Electronics (FSCFE), & Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an, 710072, China
| | - JunKang Guo
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
| | - Yongtao Li
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; College of Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China.
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13
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Bonomo MG, Calabrone L, Scrano L, Bufo SA, Di Tomaso K, Buongarzone E, Salzano G. Metagenomic monitoring of soil bacterial community after the construction of a crude oil flowline. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:48. [PMID: 34978609 PMCID: PMC8724107 DOI: 10.1007/s10661-021-09637-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/20/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to assess the metagenomic changes of soil bacterial community after constructing a crude oil flowline in Basilicata region, Italy. Soils identified a total of 56 taxa at the phylum level and 485 at the family level, with a different taxa distribution, especially in samples collected on 2014. Since microbiological diversity occurred in the soils collected after 2013 (the reference year), we performed a differential abundance analysis using DESeq2 by GAIA pipeline. In the forest area, 14 phyla and 126 families were differentially abundant (- 6.06 < logFC > 7.88) in 2014 compared to 2013. Nine families were differentially abundant in 2015, with logFC between - 3.16 and 4.66, while 20 families were significantly more abundant and 16 less abundant in 2016, with logFC between - 6.48 and 6.45. In the cultivated area, 33 phyla and 260 families showed differential abundance in 2014. In the next year (2015), 14 phyla were significantly more abundant and 19 less abundant, while 29 families were substantially more abundant and 139 less abundant, with fold changes ranging between - 5.67 and 4.01. In 2016, 33 phyla showed a significantly different abundance, as 14 were more abundant and 19 decreased, and 81 families showed a significantly increased amount with logFC between - 5.31 and 5.38. These results hypothesise that the analysed site is an altered soil where the development of particular bacterial groups attends to bioremediation processes, naturally occurring to restore optimal conditions.
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Affiliation(s)
| | - Luana Calabrone
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Laura Scrano
- Department of European Cultures, University of Basilicata, Potenza, Italy
| | - Sabino Aurelio Bufo
- Department of Sciences, University of Basilicata, Potenza, Italy
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Johannesburg, South Africa
| | - Katia Di Tomaso
- Department of Sciences, University of Basilicata, Potenza, Italy
| | | | - Giovanni Salzano
- Department of Sciences, University of Basilicata, Potenza, Italy
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14
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Maeda Y, Mise K, Iwasaki W, Watanabe A, Asakawa S, Asiloglu R, Murase J. Invention of Artificial Rice Field Soil: A Tool to Study the Effect of Soil Components on the Activity and Community of Microorganisms Involved in Anaerobic Organic Matter Decomposition. Microbes Environ 2021; 35. [PMID: 32963205 PMCID: PMC7734398 DOI: 10.1264/jsme2.me20093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Soils are characterized by diverse biotic and abiotic constituents, and this complexity hinders studies on the effects of individual soil components on microorganisms in soil. Although artificial soils have been used to overcome this issue, anoxic soils have not yet been examined. We herein aimed to create artificial soil that reproduces anaerobic methane production by soil from a rice field. Organic materials and mineral particles separated from rice field soil were mixed to prepare an artificial soil matrix; the matrix was added with a small volume of a soil suspension as a microbial inoculum. When the microbial inoculum was added immediately after matrix preparation, anaerobic decomposition was markedly less than that by original soil. When the inoculum was added 9–15 days after soil matrix preparation, anaerobic CO2 and methane production was markedly activated, similar to that by original soil after 40 days of incubation, which suggested that the maturation of the soil matrix was crucial for the reproduction of anaerobic microbial activities. The diversity of the microbial community that developed in artificial soil was markedly less than that in original soil, whereas their predicted functional profiles were similar. Humic substances altered the composition and network patterns of the microbial community. These results suggested that the functional redundancy of soil microorganisms was sustained by different microbial sub-communities. The present study demonstrated that artificial soil is a useful tool for investigating the effects of soil components on microorganisms in anoxic soil.
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Affiliation(s)
- Yu Maeda
- Graduate School of Bioagricultural Sciences, Nagoya University
| | | | | | - Akira Watanabe
- Graduate School of Bioagricultural Sciences, Nagoya University
| | - Susumu Asakawa
- Graduate School of Bioagricultural Sciences, Nagoya University
| | | | - Jun Murase
- Graduate School of Bioagricultural Sciences, Nagoya University
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15
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Hu X, Zhang T, Tian G, Zhang L, Bian B. Pilot-scale vermicomposting of sewage sludge mixed with mature vermicompost using earthworm reactor of frame composite structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144217. [PMID: 33434844 DOI: 10.1016/j.scitotenv.2020.144217] [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: 10/22/2020] [Revised: 11/22/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
To improve the efficiency of sludge vermicomposting, a new cost-effective method is provided. It uses a new earthworm reactor with a frame composite structure for vermicomposting and reuses mature vermicompost to condition the sludge. Under the optimum conditions (proportion of earthworm droppings: 15%; thickness of sludge laying: 6 cm; moisture content of initial sludge mixture: 75%), the method of continuous operation described herein works well and presents three advantages compared with the traditional vermicomposting method: the short time required for vermicomposting (20.25 h); covering a small area (5 m2/t·d); and a low cost. In addition, the vermicompost obtained from sludge vermicomposting shows better stability and maturity (C/N: 14.96; GI: 86.42%; TOC: 188.5 mg/g; ash content: 516.2 mg/g). The investigation of the associated mechanisms, including 3D-EEM, TGA, SEM and microbial community analyses, revealed that the addition of mature vermicompost can speed up the progress of decomposition and humification of organic matter in sludge. The process of vermicomposting and adding mature vermicompost significantly modified the microbial community of sewage sludge, and the changes in microorganisms in vermicompost were related to the microorganisms in the earthworm gut.
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Affiliation(s)
- Xiuren Hu
- School of Environment, Nanjing Normal University, Nanjing 210046, China
| | - Tong Zhang
- School of Environment, Nanjing Normal University, Nanjing 210046, China
| | - Ganpei Tian
- School of Environment, Nanjing Normal University, Nanjing 210046, China
| | - Limin Zhang
- School of Environment, Nanjing Normal University, Nanjing 210046, China; Green Economy Development Institute, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Bo Bian
- School of Environment, Nanjing Normal University, Nanjing 210046, China.
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16
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Yang R, Lin S, Dong Y, Ye H, Zhang T. Effect of microorganisms on the fingerprint of the volatile compounds in pine nut (Pinus koraiensis) peptide powder during storage. J Food Biochem 2021; 45:e13653. [PMID: 33792061 DOI: 10.1111/jfbc.13653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/25/2021] [Accepted: 01/31/2021] [Indexed: 11/28/2022]
Abstract
Pine nut (Pinus koraiensis) peptide (PNP) powder possesses promising bioactivities. However, the powder may have the quality problem of becoming sticky and smelly. Therefore, the volatile compounds' fingerprint of PNP powder was established by headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS). The essential spoilage microorganisms were confirmed by 16S rDNA amplicon sequencing. The antioxidant activity, which presents PNP powder's quality, decreased during storage with the highest value of (1.88 ± 0.18) × 1014 at day 30. Fifty-nine significantly changed signals were detected; eight compounds were considered as volatile marker compounds. Besides, Firmicutes and Cyanobacteria were the essential spoilage microorganisms in PNP powder at the phylum level. Significantly, unidentified_Chloroplast, which belongs to Cyanobacteria, had a positive correlation with volatile marker compounds. The results proved that microorganisms indeed affect volatile compounds of PNP powder and induced off-flavor, including hexanal, which can be used as the detection indicator for the quality control of PNP powder. PRACTICAL APPLICATIONS: In the present study, we controlled the influence of moisture migration on PNP powder and investigated microorganisms' effects on volatile compounds of PNP powder. HS-GC-IMS could be used to establish fingerprints of volatile compounds in PNP powder. 16S rDNA amplicon sequencing method could be used to screen the dominant spoilage bacteria in PNP powder and established essential spoilage microorganisms of PNP powder. This work provides a reference for category identification of PNP powder, which was infected by spoilage bacteria or not, and stored at day 0 or 30 days. Hexanal can be considered as the volatile marker compound generated from microorganisms. It helps to realize the controllability of PNP powder storage and prolongs the shelf life of PNP powder.
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Affiliation(s)
- Ruiwen Yang
- College of Food Science and Engineering, Jilin University, Changchun, P.R. China
| | - Songyi Lin
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, P.R. China
| | - Yifei Dong
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, P.R. China
| | - Haiqing Ye
- College of Food Science and Engineering, Jilin University, Changchun, P.R. China
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, P.R. China
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17
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Sasaki K, Sasaki D, Tsuge Y, Morita M, Kondo A. Enhanced methane production from cellulose using a two-stage process involving a bioelectrochemical system and a fixed film reactor. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:7. [PMID: 33407783 PMCID: PMC7789537 DOI: 10.1186/s13068-020-01866-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND It is desirable to improve the anaerobic digestion processes of recalcitrant materials, such as cellulose. Enhancement of methane (CH4) production from organic molecules was previously accomplished through coupling a bioelectrochemical system (BES); however, scaling-up BES-based production is difficult. Here, we developed a two-stage process consisting of a BES using low-cost and low-reactive carbon sheets as the cathode and anode, and a fixed film reactor (FFR) containing conductive material, i.e., carbon fiber textiles (CFTs) (:BES → FFR). By controlling the cathodic current at 2.7 μA/cm2 without abiotic H2 production, the three-electrode BES system was operated to mimic a microbial electrolysis cell. RESULTS The thermophilic BES (inlet pH: 6.1) and FFR (inlet pH: 7.5) were operated using hydraulic retention times (HRTs) of 2.5 and 4.2 days, respectively, corresponding to a cellulose load of 3555.6 mg-carbon (C)/(L day). The BES → FFR process achieved a higher CH4 yield (37.5%) with 52.8 vol% CH4 in the product gas compared to the non-bioelectrochemical system (NBES) → FFR process, which showed a CH4 yield of 22.1% with 46.8 vol% CH4. The CH4 production rate (67.5 mM/day) obtained with the BER → FFR process was much higher than that obtained using electrochemical methanogenesis (0.27 mM/day). Application of the electrochemical system or CFTs improved the yields of CH4 with the NBES → FFR or BES → non-fixed film reactor process, respectively. Meta 16S rRNA sequencing revealed that putative cellulolytic bacteria (identified as Clostridium species) were present in the BES and NBES, and followed (BES→ and NBES→) FFR. Notably, H2-consuming methanogens, Methanobacterium sp. and Methanosarcina sp., showed increased relative abundances in the suspended fraction and attached fraction of (BES→) FFR, respectively, compared to that of (NBES→) FFR, although these methanogens were observed at trace levels in the BES and NBES. CONCLUSIONS These results indicate that bioelectrochemical preprocessing at a low current effectively induces interspecies H2 transfer in the FFR with conductive material. Sufficient electrochemical preprocessing was observed using a relatively short HRT. This type of two-stage process, BES → FFR, is useful for stabilization and improvement of the biogas (CH4) production from cellulosic material, and our results imply that the two-stage system developed here may be useful with other recalcitrant materials.
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Affiliation(s)
- Kengo Sasaki
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.
| | - Daisuke Sasaki
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Yota Tsuge
- Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Masahiko Morita
- Environment Chemistry Sector, Environmental Science Research Laboratory, Central Research Institute of Electric Power Industry, 1646 Abiko, Abiko-shi, Chiba-ken, 270-1194, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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18
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Bornbusch SL, Grebe NM, Lunn S, Southworth CA, Dimac-Stohl K, Drea C. Stable and transient structural variation in lemur vaginal, labial and axillary microbiomes: patterns by species, body site, ovarian hormones and forest access. FEMS Microbiol Ecol 2020; 96:5836713. [PMID: 32401310 DOI: 10.1093/femsec/fiaa090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/12/2020] [Indexed: 01/01/2023] Open
Abstract
Host-associated microbiomes shape and are shaped by myriad processes that ultimately delineate their symbiotic functions. Whereas a host's stable traits, such as its lineage, relate to gross aspects of its microbiome structure, transient factors, such as its varying physiological state, relate to shorter term, structural variation. Our understanding of these relationships in primates derives principally from anthropoid studies and would benefit from a broader, comparative perspective. We thus examined the vaginal, labial and axillary microbiota of captive, female ring-tailed lemurs (Lemur catta) and Coquerel's sifakas (Propithecus coquereli), across an ovarian cycle, to better understand their relation to stable (e.g. species identity/mating system, body site) and transient (e.g. ovarian hormone concentration, forest access) host features. We used 16S amplicon sequencing to determine microbial composition and enzyme-linked immunosorbent assays to measure serum hormone concentrations. We found marked variation in microbiota diversity and community composition between lemur species and their body sites. Across both host species, microbial diversity was significantly correlated with ovarian hormone concentrations: negatively with progesterone and positively with estradiol. The hosts' differential forest access related to the diversity of environmental microbes, particularly in axillary microbiomes. Such transient endogenous and exogenous modulators have potential implications for host reproductive health and behavioral ecology.
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Affiliation(s)
| | - Nicholas M Grebe
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Siera Lunn
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Kristin Dimac-Stohl
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Christine Drea
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Department of Biology, Duke University, Durham, NC 27708, USA
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19
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Meier MJ, Dodge AE, Samarajeewa AD, Beaudette LA. Soil exposed to silver nanoparticles reveals significant changes in community structure and altered microbial transcriptional profiles. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113816. [PMID: 31864930 DOI: 10.1016/j.envpol.2019.113816] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/09/2019] [Accepted: 12/13/2019] [Indexed: 05/20/2023]
Abstract
Anthropogenic activities can disrupt soil ecosystems, normally resulting in reduced soil microbial health. Regulatory agencies need to determine the effects of uncharacterized substances on soil microbial health to establish the safety of these chemicals if they end up in the environment. Previous work has focused on measuring traditional ecotoxicologial endpoints within the categories of microbial biomass, activity, and community structure/diversity. Because these tests can be labor intensive, lengthy to conduct, and cannot measure changes in individual gene functions, we wanted to establish whether metatranscriptomics could be used as a more sensitive endpoint and provide a perspective on community function that is more informative than taxonomic identification of microbes alone. We spiked a freshly collected sandy loam soil (Vulcan, Alberta, Canada) with 0, 60, 145, 347, 833, and 2000 mg kg-1 of silver nanoparticles (AgNPs), a known antagonist of microorganisms due to its propensity for dissolution of toxic silver ions. Assessments performed in our previous work using traditional tests demonstrated the toxicity of AgNPs on soil microbial processes. We expanded this analysis with genomics-based tests by measuring changes in community taxonomic structure and function using 16S rDNA profiling and metatranscriptomics. In addition to identifying bacterial taxa affected by AgNPs, we found that genes involved in heavy metal resistance (e.g., the CzcA efflux pump) and other toxicity response pathways were highly upregulated in the presence of silver. Dose-response analysis using BMDExpress2 software successfully modeled many physiologically relevant genes responding to low concentrations of AgNPs. We found that the transcriptomic point of departure (BMD50) was lower than the IC50s calculated using the traditional tests in our previous work. These results suggest that dose-response modeling of metatranscriptomic gene expression is a useful tool in soil microbial health assessment. SUMMARY: Genomics-based endpoints for the assessment of soil microbial health can be used to perform quantitative dose-response modeling, and soil-based RNAseq adds functional insights.
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Affiliation(s)
- Matthew J Meier
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada.
| | - Annette E Dodge
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
| | - Ajith Dias Samarajeewa
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
| | - Lee A Beaudette
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
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20
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Mao H, Zhang H, Fu Q, Zhong M, Li R, Zhai B, Wang Z, Zhou L. Effects of four additives in pig manure composting on greenhouse gas emission reduction and bacterial community change. BIORESOURCE TECHNOLOGY 2019; 292:121896. [PMID: 31404757 DOI: 10.1016/j.biortech.2019.121896] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
Four different additives of Medical stone (MS), Zeolite (ZL), Bamboo biochar (BC), and Wood vinegar (WV) were investigated in pig manure composting. The four additives reduced the peak CH4 emission from 54% to 74%, while reduced N2O loss from 36% to 69%, compared with control (CK). WV and ZL showed better ability in N2O loss reduction, yet MS with the efficient inhibition both on CH4 and NH3 emissions. The bacterial community analysis indicated that bacterial diversity in the maturity phase was higher than that in the thermophilic phase, especially with treatments of ZL, BC and WV. The selected factors of pH, temperature, TOC and DOC could influence the thermophilic phase, while EC and TKN related closely with maturity phase in pig manure composting.
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Affiliation(s)
- Hui Mao
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Haoyue Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qian Fu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Minzheng Zhong
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ronghua Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Bingnian Zhai
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Zhaohui Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Lina Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China.
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21
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Wieczorek AS, Schmidt O, Chatzinotas A, von Bergen M, Gorissen A, Kolb S. Ecological Functions of Agricultural Soil Bacteria and Microeukaryotes in Chitin Degradation: A Case Study. Front Microbiol 2019; 10:1293. [PMID: 31281293 PMCID: PMC6596343 DOI: 10.3389/fmicb.2019.01293] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/23/2019] [Indexed: 11/24/2022] Open
Abstract
Chitin provides a valuable carbon and nitrogen source for soil microorganisms and is a major component of particulate organic matter in agricultural soils. To date, there is no information on interaction and interdependence in chitin-degrading soil microbiomes. Since microbial chitin degradation occurs under both oxic and anoxic conditions and both conditions occur simultaneously in soil, the comparison of the active microbiome members under both conditions can reveal key players for the overall degradation in aerated soil. A time-resolved 16S rRNA stable isotope probing experiment was conducted with soil material from the top soil layer of a wheat-covered field. [13CU]-chitin was largely mineralized within 20 days under oxic conditions. Cellvibrio, Massilia, and several Bacteroidetes families were identified as initially active chitin degraders. Subsequently, Planctomycetes and Verrucomicrobia were labeled by assimilation of 13C carbon either from [13CU]-chitin or from 13C-enriched components of primary chitin degraders. Bacterial predators (e.g., Bdellovibrio and Bacteriovorax) were labeled, too, and non-labeled microeukaryotic predators (Alveolata) increased their relative abundance toward the end of the experiment (70 days), indicating that chitin degraders were subject to predation. Trophic interactions differed substantially under anoxic and oxic conditions. Various fermentation types occurred along with iron respiration. While Acidobacteria and Chloroflexi were the first taxa to be labeled, although at a low 13C level, Firmicutes and uncultured Bacteroidetes were predominantly labeled at a much higher 13C level during the later stages, suggesting that the latter two bacterial taxa were mainly responsible for the degradation of chitin and also provided substrates for iron reducers. Eventually, our study revealed that (1) hitherto unrecognized Bacteria were involved in a chitin-degrading microbial food web of an agricultural soil, (2) trophic interactions were substantially shaped by the oxygen availability, and (3) detectable predation was restricted to oxic conditions. The gained insights into trophic interactions foster our understanding of microbial chitin degradation, which is in turn crucial for an understanding of soil carbon dynamics.
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Affiliation(s)
- Adam S Wieczorek
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Leipzig, Germany.,Department of Chemistry and Bioscience, University of Aalborg, Aalborg, Denmark
| | | | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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22
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Liu P, Klose M, Conrad R. Temperature-Dependent Network Modules of Soil Methanogenic Bacterial and Archaeal Communities. Front Microbiol 2019; 10:496. [PMID: 30915063 PMCID: PMC6422946 DOI: 10.3389/fmicb.2019.00496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/26/2019] [Indexed: 11/13/2022] Open
Abstract
Temperature is an important factor regulating the production of the greenhouse gas CH4. Structure and function of the methanogenic microbial communities are often drastically different upon incubation at 45°C versus 25°C or 35°C, but are also different in different soils. However, the extent of taxonomic redundancy within each functional group and the existence of different temperature-dependent microbial community network modules are unknown. Therefore, we investigated paddy soils from Italy and the Philippines and a desert soil from Utah (United States), which all expressed CH4 production upon flooding and exhibited structural and functional differences upon incubation at three different temperatures. We continued incubation of the pre-incubated soils (Liu et al., 2018) by changing the temperature in a factorial manner. We determined composition, abundance and function of the methanogenic archaeal and bacterial communities using HiSeq Illumina sequencing, qPCR and analysis of activity and stable isotope fractionation, respectively. Heatmap analysis of operational taxonomic units (OTU) from the different incubations gave detailed insights into the community structures and their putative functions. Network analysis showed that the microbial communities in the different soils were all organized within modules distinct for the three incubation temperatures. The diversity of Bacteria and Archaea was always lower at 45°C than at 25 or 35°C. A shift from 45°C to lower temperatures did not recover archaeal diversity, but nevertheless resulted in the establishment of structures and functions that were largely typical for soil at moderate temperatures. At 25 and 35°C and after shifting to one of these temperatures, CH4 was always produced by a combination of acetoclastic and hydrogenotrophic methanogenesis being consistent with the presence of acetoclastic (Methanosarcinaceae, Methanotrichaceae) and hydrogenotrophic (Methanobacteriales, Methanocellales, Methanosarcinaceae) methanogens. At 45°C, however, or after shifting from moderate temperatures to 45°C, only the Philippines soil maintained such combination, while the other soils were devoid of acetoclastic methanogens and consumed acetate instead by syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis. Syntrophic acetate oxidation was apparently achieved by Thermoanaerobacteraceae, which were especially abundant in Italian paddy soil and Utah desert soil when incubated at 45°C. Other bacterial taxa were also differently abundant at 45°C versus moderate temperatures, as seen by the formation of specific network modules. However, the archaeal OTUs with putative function in acetoclastic or hydrogenotrophic methanogenesis as well as the bacterial OTUs were usually not identical across the different soils and incubation conditions, and if they were, they suggested the existence of mesophilic and thermophilic ecotypes within the same OTUs. Overall, methanogenic function was determined by the bacterial and/or archaeal community structures, which in turn were to quite some extent determined by the incubation temperature, albeit largely individually in each soil. There was quite some functional redundancy as seen by different taxonomic community structures in the different soils and at the different temperatures.
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Affiliation(s)
- Pengfei Liu
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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23
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Wegner CE, Gaspar M, Geesink P, Herrmann M, Marz M, Küsel K. Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon. Appl Environ Microbiol 2019; 85:e02346-18. [PMID: 30578263 PMCID: PMC6384109 DOI: 10.1128/aem.02346-18] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/14/2018] [Indexed: 11/20/2022] Open
Abstract
Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbor autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-omic profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes, and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, and ammonium oxidation [anammox]) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), depending on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Being dominated by a few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, and Thaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes encoded by different microbiome members, along with the groundwater flow path. The turnover of organic carbon apparently complements for lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome depending on the availability of oxygen and inorganic electron donors, like ammonium.IMPORTANCE Groundwater is a key resource for drinking water production and irrigation. The interplay between geological setting, hydrochemistry, carbon storage, and groundwater microbiome ecosystem functioning is crucial for our understanding of these important ecosystem services. We targeted the encoded and expressed metabolic potential of groundwater microbiomes along an aquifer transect that diversifies in terms of hydrochemistry and land use. Our results showed that the groundwater microbiome has a higher spatial differentiation potential than does hydrochemistry.
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Affiliation(s)
- Carl-Eric Wegner
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Michael Gaspar
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, Jena, Germany
| | - Patricia Geesink
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Martina Herrmann
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, Jena, Germany
- Leibniz Institute on Aging, Fritz Lipman Institute, Jena, Germany
| | - Kirsten Küsel
- Chair of Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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24
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Dang C, Morrissey EM, Neubauer SC, Franklin RB. Novel microbial community composition and carbon biogeochemistry emerge over time following saltwater intrusion in wetlands. GLOBAL CHANGE BIOLOGY 2019; 25:549-561. [PMID: 30537235 DOI: 10.1111/gcb.14486] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/14/2018] [Indexed: 06/09/2023]
Abstract
Sea level rise and changes in precipitation can cause saltwater intrusion into historically freshwater wetlands, leading to shifts in microbial metabolism that alter greenhouse gas emissions and soil carbon sequestration. Saltwater intrusion modifies soil physicochemistry and can immediately affect microbial metabolism, but further alterations to biogeochemical processing can occur over time as microbial communities adapt to the changed environmental conditions. To assess temporal changes in microbial community composition and biogeochemical activity due to saltwater intrusion, soil cores were transplanted from a tidal freshwater marsh to a downstream mesohaline marsh and periodically sampled over 1 year. This experimental saltwater intrusion produced immediate changes in carbon mineralization rates, whereas shifts in the community composition developed more gradually. Salinity affected the composition of the prokaryotic community but did not exert a strong influence on the community composition of fungi. After only 1 week of saltwater exposure, carbon dioxide production doubled and methane production decreased by three orders of magnitude. By 1 month, carbon dioxide production in the transplant was comparable to the saltwater controls. Over time, we observed a partial recovery in methane production which strongly correlated with an increase in the relative abundance of three orders of hydrogenotrophic methanogens. Taken together, our results suggest that ecosystem responses to saltwater intrusion are dynamic over time as complex interactions develop between microbial communities and the soil organic carbon pool. The gradual changes in microbial community structure we observed suggest that previously freshwater wetlands may not experience an equilibration of ecosystem function until long after initial saltwater intrusion. Our results suggest that during this transitional period, likely lasting years to decades, these ecosystems may exhibit enhanced greenhouse gas production through greater soil respiration and continued methanogenesis.
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Affiliation(s)
- Chansotheary Dang
- Plant and Soil Sciences, South Agricultural Sciences Building, West Virginia University, Morgantown, West Virginia
- Department of Biology, Trani Center for Life Sciences, Virginia Commonwealth University, Richmond, Virginia
| | - Ember M Morrissey
- Plant and Soil Sciences, South Agricultural Sciences Building, West Virginia University, Morgantown, West Virginia
| | - Scott C Neubauer
- Department of Biology, Trani Center for Life Sciences, Virginia Commonwealth University, Richmond, Virginia
| | - Rima B Franklin
- Department of Biology, Trani Center for Life Sciences, Virginia Commonwealth University, Richmond, Virginia
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25
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Peng J, Wegner CE, Bei Q, Liu P, Liesack W. Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil. MICROBIOME 2018; 6:169. [PMID: 30231929 PMCID: PMC6147125 DOI: 10.1186/s40168-018-0546-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/31/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND The expected increase in global surface temperature due to climate change may have a tremendous effect on the structure and function of the anaerobic food web in flooded rice field soil. Here, we used the metatranscriptomic analysis of total RNA to gain a system-level understanding of this temperature effect on the methanogenic food web. RESULTS Mesophilic (30 °C) and thermophilic (45 °C) food web communities had a modular structure. Family-specific rRNA dynamics indicated that each network module represents a particular function within the food webs. Temperature had a differential effect on all the functional activities, including polymer hydrolysis, syntrophic oxidation of key intermediates, and methanogenesis. This was further evidenced by the temporal expression patterns of total bacterial and archaeal mRNA and of transcripts encoding carbohydrate-active enzymes (CAZymes). At 30 °C, various bacterial phyla contributed to polymer hydrolysis, with Firmicutes decreasing and non-Firmicutes (e.g., Bacteroidetes, Ignavibacteriae) increasing with incubation time. At 45 °C, CAZyme expression was solely dominated by the Firmicutes but, depending on polymer and incubation time, varied on family level. The structural and functional community dynamics corresponded well to process measurements (acetate, propionate, methane). At both temperatures, a major change in food web functionality was linked to the transition from the early to late stage. The mesophilic food web was characterized by gradual polymer breakdown that governed acetoclastic methanogenesis (Methanosarcinaceae) and, with polymer hydrolysis becoming the rate-limiting step, syntrophic propionate oxidation (Christensenellaceae, Peptococcaceae). The thermophilic food web had two activity stages characterized first by polymer hydrolysis and followed by syntrophic oxidation of acetate (Thermoanaerobacteraceae, Heliobacteriaceae, clade OPB54). Hydrogenotrophic Methanocellaceae were the syntrophic methanogen partner, but their population structure differed between the temperatures. Thermophilic temperature promoted proliferation of a new Methanocella ecotype. CONCLUSIONS Temperature had a differential effect on the structural and functional continuum in which the methanogenic food web operates. This temperature-induced change in food web functionality may not only be a near-future scenario for rice paddies but also for natural wetlands in the tropics and subtropics.
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Affiliation(s)
- Jingjing Peng
- Research Group Methanotrophic Bacteria and Environmental Genomics/Transcriptomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Carl-Eric Wegner
- Institute of Ecology, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Str. 159, 07749, Jena, Germany
| | - Qicheng Bei
- Research Group Methanotrophic Bacteria and Environmental Genomics/Transcriptomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Pengfei Liu
- Research Group Methanotrophic Bacteria and Environmental Genomics/Transcriptomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Werner Liesack
- Research Group Methanotrophic Bacteria and Environmental Genomics/Transcriptomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany.
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26
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Zhan Y, Liu W, Bao Y, Zhang J, Petropoulos E, Li Z, Lin X, Feng Y. Fertilization shapes a well-organized community of bacterial decomposers for accelerated paddy straw degradation. Sci Rep 2018; 8:7981. [PMID: 29789525 PMCID: PMC5964224 DOI: 10.1038/s41598-018-26375-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/02/2018] [Indexed: 11/09/2022] Open
Abstract
Straw, mainly dry stalks of crops, is an agricultural byproduct. Its incorporation to soils via microbial redistribution is an environment-friendly way to increase fertility. Fertilization influences soil microorganisms and straw degradation. However, our up to date knowledge on the responses of the straw decomposers to fertilization remains elusive. To this end, inoculated with paddy soils with 26-year applications of chemical fertilizers, organic amendments or controls without fertilization, microcosms were anoxically incubated with 13C-labelled rice straw amendment. DNA-based stable isotope probing and molecular ecological network analysis were conducted to unravel how straw degrading bacterial species shift in responses to fertilizations, as well as evaluate what their roles/links in the microbiome are. It was found that only a small percentage of the community ecotypes was participating into straw degradation under both fertilizations. Fertilization, especially with organic amendments decreased the predominance of Firmicutes- and Acidobacteria-like straw decomposers but increased those of the copiotrophs, such as β-Proteobacteria and Bacteroidetes due to increased soil fertility. For the same reason, fertilization shifted the hub species towards those of high degrading potential and created a more stable and efficient microbial consortium. These findings indicate that fertilization shapes a well-organized community of decomposers for accelerated straw degradation.
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Affiliation(s)
- Yushan Zhan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, P.R. China
| | - Wenjing Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, P.R. China
| | - Yuanyuan Bao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, P.R. China
| | - Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, P.R. China
| | - Evangelos Petropoulos
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, P.R. China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, P.R. China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, P.R. China.
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27
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Liao H, Chapman SJ, Li Y, Yao H. Dynamics of microbial biomass and community composition after short-term water status change in Chinese paddy soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:2932-2941. [PMID: 29147983 DOI: 10.1007/s11356-017-0690-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
Paddy soil experiences repeated anaerobic and aerobic changes during rice growth, the dramatic dynamics of soil water status accompanied by changes in redox condition and O2 availability. However, the effect of rapid water status change on soil microbial biomass and community composition is not well explored. Here, we present a comprehensive study focusing on the short-term water status change in 13 Chinese paddy soils. In order to gain a reliable way to determine soil microbial biomass carbon (MBC) in flooded or water-saturated soils, we also evaluated two different procedures (nitrogen bubbled and 100 °C water bath) to remove chloroform in extracts during the fumigation process. Compared to non-flooded paddy soils, the flooded paddy soils tended to have a lower microbial biomass, and this was much clearer using adenosine 5'-triphosphate (ATP) and phospholipid fatty acid (PLFA) analysis compared to biomass measured by the fumigation method. Fungal biomass, which was indicated by both ergosterol and the PLFA 18:2ω6,9c, also decreased after short-term flooding. Changes in soil microbial community composition (determined by PLFA biomarkers) were observed after short-term flooding, but the extent varied between soils. This study indicates that the dynamics of short-term water status altered the soil microbial biomass (ATP, MBC, and total PLFA) and community composition. Finally, our results suggested that liquid fumigation combined with the nitrogen-bubbled method is the best choice for analyzing MBC concentrations in water-saturated soils.
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Affiliation(s)
- Hongkai Liao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China
- Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo, 315800, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | | | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China
- Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo, 315800, People's Republic of China
| | - Huaiying Yao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.
- Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, Ningbo, 315800, People's Republic of China.
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430073, People's Republic of China.
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28
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Wojcieszak M, Pyzik A, Poszytek K, Krawczyk PS, Sobczak A, Lipinski L, Roubinek O, Palige J, Sklodowska A, Drewniak L. Adaptation of Methanogenic Inocula to Anaerobic Digestion of Maize Silage. Front Microbiol 2017; 8:1881. [PMID: 29033919 PMCID: PMC5625012 DOI: 10.3389/fmicb.2017.01881] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/14/2017] [Indexed: 11/24/2022] Open
Abstract
A well-balanced microbial consortium is crucial for efficient biogas production. In turn, one of a major factor that influence on the structure of anaerobic digestion (AD) consortium is a source of microorganisms which are used as an inoculum. This study evaluated the influence of inoculum sources (with various origin) on adaptation of a biogas community and the efficiency of the biomethanization of maize silage. As initial inocula for AD of maize silage the samples from: (i) an agricultural biogas plant (ABP) which utilizes maize silage as a main substrate, (ii) cattle slurry (CS), which contain elevated levels of lignocelluloses materials, and (iii) raw sewage sludge (RSS) with low content of plant origin materials were used. The adaptation of methanogenic consortia was monitored during a series of passages, and the functionality of the adapted consortia was verified through start-up operation of AD in two-stage reactors. During the first stages of the adaptation phase, methanogenic consortia occurred very slowly, and only after several passages did the microbial community adapts to allow production of biogas with high methane content. The ABP consortium revealed highest biogas production in the adaptation and in the start-up process. The biodiversity dynamics monitored during adaptation and start-up process showed that community profile changed in a similar direction in three studied consortia. Native communities were very distinct to each other, while at the end of the Phase II of the start-up process microbial diversity profile was similar in all consortia. All adopted bacterial communities were dominated by representatives of Porphyromonadaceae, Rikenellaceae, Ruminococcaceae, and Synergistaceae. A shift from low acetate-preferring acetoclastic Methanosaetaceae (ABP and RSS) and/or hydrogenotrophic Archaea, e.g., Methanomicrobiaceae (CS) prevailing in the inoculum samples to larger populations of high acetate-preferring acetoclastic Methanosarcinaceae was observed by the end of the experiment. As a result, three independent, functional communities that syntrophically produced methane from acetate (primarily) and H2/CO2, methanol and methylamines were adapted. This study provides new insights into the specific process by which different inocula sampled from typical methanogenic environments that are commonly used to initiate industrial installations gradually adapted to allow biogas production from maize silage.
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Affiliation(s)
- Martyna Wojcieszak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Adam Pyzik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Krzysztof Poszytek
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Pawel S Krawczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Adam Sobczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Otton Roubinek
- Institute of Nuclear Chemistry and Technology, Warsaw, Poland
| | - Jacek Palige
- Institute of Nuclear Chemistry and Technology, Warsaw, Poland
| | - Aleksandra Sklodowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Reim A, Hernández M, Klose M, Chidthaisong A, Yuttitham M, Conrad R. Response of Methanogenic Microbial Communities to Desiccation Stress in Flooded and Rain-Fed Paddy Soil from Thailand. Front Microbiol 2017; 8:785. [PMID: 28529503 PMCID: PMC5418361 DOI: 10.3389/fmicb.2017.00785] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/18/2017] [Indexed: 11/24/2022] Open
Abstract
Rice paddies in central Thailand are flooded either by irrigation (irrigated rice) or by rain (rain-fed rice). The paddy soils and their microbial communities thus experience permanent or arbitrary submergence, respectively. Since methane production depends on anaerobic conditions, we hypothesized that structure and function of the methanogenic microbial communities are different in irrigated and rain-fed paddies and react differently upon desiccation stress. We determined rates and relative proportions of hydrogenotrophic and aceticlastic methanogenesis before and after short-term drying of soil samples from replicate fields. The methanogenic pathway was determined by analyzing concentrations and δ13C of organic carbon and of CH4 and CO2 produced in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis. We also determined the abundance (qPCR) of genes and transcripts of bacterial 16S rRNA, archaeal 16S rRNA and methanogenic mcrA (coding for a subunit of the methyl coenzyme M reductase) and the composition of these microbial communities by T-RFLP fingerprinting and/or Illumina deep sequencing. The abundances of genes and transcripts were similar in irrigated and rain-fed paddy soil. They also did not change much upon desiccation and rewetting, except the transcripts of mcrA, which increased by more than two orders of magnitude. In parallel, rates of CH4 production also increased, in rain-fed soil more than in irrigated soil. The contribution of hydrogenotrophic methanogenesis increased in rain-fed soil and became similar to that in irrigated soil. However, the relative microbial community composition on higher taxonomic levels was similar between irrigated and rain-fed soil. On the other hand, desiccation and subsequent anaerobic reincubation resulted in systematic changes in the composition of microbial communities for both Archaea and Bacteria. It is noteworthy that differences in the community composition were mostly detected on the level of operational taxonomic units (OTUs; 97% sequence similarity). The treatments resulted in change of the relative abundance of several archaeal OTUs. Some OTUs of Methanobacterium, Methanosaeta, Methanosarcina, Methanocella and Methanomassiliicoccus increased, while some of Methanolinea and Methanosaeta decreased. Bacterial OTUs within Firmicutes, Cyanobacteria, Planctomycetes and Deltaproteobacteria increased, while OTUs within other proteobacterial classes decreased.
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Affiliation(s)
- Andreas Reim
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
| | - Marcela Hernández
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany.,Centre for Biological Sciences, University of SouthamptonSouthampton, UK
| | - Melanie Klose
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
| | - Amnat Chidthaisong
- Joint Graduate School of Energy and Environment, King Mongkut's University of Technology ThonburiBangkok, Thailand
| | - Monthira Yuttitham
- Faculty of Environment and Resource Studies, Mahidol UniversitySalaya, Thailand
| | - Ralf Conrad
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
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30
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Peng J, Wegner CE, Liesack W. Short-Term Exposure of Paddy Soil Microbial Communities to Salt Stress Triggers Different Transcriptional Responses of Key Taxonomic Groups. Front Microbiol 2017; 8:400. [PMID: 28400748 PMCID: PMC5368272 DOI: 10.3389/fmicb.2017.00400] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 02/27/2017] [Indexed: 11/30/2022] Open
Abstract
Soil salinization due to seawater intrusion along coastal areas is an increasing threat to rice cultivation worldwide. While the detrimental impact on rice growth and yield has been thoroughly studied, little is known about how severe salinity affects structure and function of paddy soil microbial communities. Here, we examined their short-term responses to half- and full-strength seawater salinity in controlled laboratory experiments. Slurry microcosms were incubated under anoxic conditions, with rice straw added as carbon source. Stress exposure time was for 2 days after a pre-incubation period of 7 days. Relative to the control, moderate (300 mM NaCl) and high (600 mM NaCl) salt stress suppressed both net consumption of acetate and methane production by 50% and 70%, respectively. Correspondingly, community-wide mRNA expression decreased by 50–65%, with significant changes in relative transcript abundance of family-level groups. mRNA turnover was clearly more responsive to salt stress than rRNA dynamics. Among bacteria, Clostridiaceae were most abundant and the only group whose transcriptional activity was strongly stimulated at 600 mM NaCl. In particular, clostridial mRNA involved in transcription/translation, fermentation, uptake and biosynthesis of compatible solutes, and flagellar motility was significantly enriched in response salt stress. None of the other bacterial groups were able to compete at 600 mM NaCl. Their responses to 300 mM NaCl were more diverse. Lachnospiraceae increased, Ruminococcaceae maintained, and Peptococcaceae, Veillonellaceae, and Syntrophomonadaceae decreased in relative mRNA abundance. Among methanogens, Methanosarcinaceae were most dominant. Relative to other family-level groups, salt stress induced a significant enrichment of transcripts related to the CO dehydrogenase/acetyl-coenzyme A synthase complex, methanogenesis, heat shock, ammonium uptake, and thermosomes, but the absolute abundance of methanosarcinal mRNA decreased. Most strikingly, the transcriptional activity of the Methanocellaceae was completely suppressed already at 300 mM NaCl. Apparently, the key taxonomic groups involved in the methanogenic breakdown of plant polymers significantly differ in their ability to cope with severe salt stress. Presumably, this different ability is directly linked to differences in their genetic potential and metabolic flexibility to reassign available energy resources for cellular adaptation to salt stress.
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Affiliation(s)
- Jingjing Peng
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Carl-Eric Wegner
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Werner Liesack
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
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Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios. Appl Environ Microbiol 2017; 83:AEM.02533-16. [PMID: 27913414 DOI: 10.1128/aem.02533-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/28/2016] [Indexed: 11/20/2022] Open
Abstract
Northern peatlands in general have high methane (CH4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient-poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO2 to CH4 produced. After [13C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH4 and CO2 The oligotrophic fen had lower CH4 production but produced 3 to 59 times more CO2 than CH4 RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO2 production in peatlands. IMPORTANCE Peatlands are major sources of the greenhouse gas methane (CH4), yet in many peatlands, CO2 production from unresolved anaerobic processes exceeds CH4 production. Anaerobic degradation produces the precursors of CH4 production but also represents competing processes. We show that anaerobic degradation leading to high or low CH4 production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH4 production, while novel and unconventional degraders could be identified in a site where CO2 production greatly exceeds CH4 production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH4 production and reveal bacteria potentially producing the excess CO2 in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH4 emission from peatlands.
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Karas PA, Perruchon C, Karanasios E, Papadopoulou ES, Manthou E, Sitra S, Ehaliotis C, Karpouzas DG. Integrated biodepuration of pesticide-contaminated wastewaters from the fruit-packaging industry using biobeds: Bioaugmentation, risk assessment and optimized management. JOURNAL OF HAZARDOUS MATERIALS 2016; 320:635-644. [PMID: 27501880 DOI: 10.1016/j.jhazmat.2016.07.071] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/02/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
Wastewaters from fruit-packaging plants contain high loads of toxic and persistent pesticides and should be treated on site. We evaluated the depuration performance of five pilot biobeds against those effluents. In addition we tested bioaugmentation with bacterial inocula as a strategy for optimization of their depuration capacity. Finally we determined the composition and functional dynamics of the microbial community via q-PCR. Practical issues were also addressed including the risk associated with the direct environmental disposal of biobed-treated effluents and decontamination methods for the spent packing material. Biobeds showed high depuration capacity (>99.5%) against all pesticides with bioaugmentation maximizing their depuration performance against the persistent fungicide thiabendazole (TBZ). This was followed by a significant increase in the abundance of bacteria, fungi and of catabolic genes of aromatic compounds catA and pcaH. Bioaugmentation was the most potent decontamination method for spent packing material with composting being an effective alternative. Risk assessment based on practical scenarios (pome and citrus fruit-packaging plants) and the depuration performance of the pilot biobeds showed that discharge of the treated effluents into an 0.1-ha disposal site did not entail an environmental risk, except for TBZ-containing effluents where a larger disposal area (0.2ha) or bioaugmentation alleviated the risk.
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Affiliation(s)
- Panagiotis A Karas
- University of Thessaly, Department of Biochemistry and Biotechnology, Ploutonos 26 and Aiolou, 41221 Larissa, Greece
| | - Chiara Perruchon
- University of Thessaly, Department of Biochemistry and Biotechnology, Ploutonos 26 and Aiolou, 41221 Larissa, Greece
| | | | - Evangelia S Papadopoulou
- University of Thessaly, Department of Biochemistry and Biotechnology, Ploutonos 26 and Aiolou, 41221 Larissa, Greece
| | - Elena Manthou
- University of Thessaly, Department of Biochemistry and Biotechnology, Ploutonos 26 and Aiolou, 41221 Larissa, Greece
| | - Stefania Sitra
- University of Thessaly, Department of Biochemistry and Biotechnology, Ploutonos 26 and Aiolou, 41221 Larissa, Greece
| | - Constantinos Ehaliotis
- Agricultural University of Athens, Department of Natural Resources and Agricultural Engineering, Laboratory of Soils and Agricultural Chemistry, 75 IeraOdos Str., 11855 Athens, Greece
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Ploutonos 26 and Aiolou, 41221 Larissa, Greece.
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33
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Ivanova AA, Wegner CE, Kim Y, Liesack W, Dedysh SN. Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis. Mol Ecol 2016; 25:4818-35. [DOI: 10.1111/mec.13806] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 06/12/2016] [Accepted: 08/11/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Anastasia A. Ivanova
- Winogradsky Institute of Microbiology; Research Center of Biotechnology of the Russian Academy of Sciences; 33, bld. 2 Leninsky Ave. Moscow 119071 Russia
| | - Carl-Eric Wegner
- Max Planck Institute for Terrestrial Microbiology; D-35043 Marburg Germany
| | - Yongkyu Kim
- Max Planck Institute for Terrestrial Microbiology; D-35043 Marburg Germany
| | - Werner Liesack
- Max Planck Institute for Terrestrial Microbiology; D-35043 Marburg Germany
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology; Research Center of Biotechnology of the Russian Academy of Sciences; 33, bld. 2 Leninsky Ave. Moscow 119071 Russia
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34
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Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil. Appl Microbiol Biotechnol 2016; 100:5989-98. [PMID: 26923143 DOI: 10.1007/s00253-016-7377-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 01/31/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
Abstract
Nitrogen fertilization and returning straw to paddy soil are important factors that regulate CH4 production. To evaluate the effect of rice straw and/or nitrate amendment on methanogens, a paddy soil was anaerobically incubated for 40 days. The results indicated that while straw addition increased CH4 production and the abundances of mcrA genes and their transcripts, nitrate amendment showed inhibitory effects on them. The terminal restriction fragment length polymorphism (T-RFLP) analysis based on mcrA gene revealed that straw addition obviously changed methanogenic community structure. Based on mcrA gene level, straw-alone addition stimulated Methanosarcinaceaes at the early stage of incubation (first 11 days), but nitrate showed inhibitory effect. The relative abundance of Methanobacteriaceae was also stimulated by straw addition during the first 11 days. Furthermore, Methanosaetaceae were enriched by nitrate-alone addition after 11 days, while Methanocellaceae were enriched by nitrate addition especially within the first 5 days. The transcriptional methanogenic community indicated more dynamic and complicated responses to straw and/or nitrate addition. Based on mcrA transcript level, nitrate addition alone resulted in the increase of Methanocellaceae and the shift from Methanosarcinaceae to Methanosaetaceae during the first 5 days of incubation. Straw treatments increased the relative abundance of Methanobacteriaceae after 11 days. These results demonstrate that nitrate addition influences methanogens which are transcriptionally and functionally active and can alleviate CH4 production associated with straw amendment in paddy soil incubations, presumably through competition for common substrates between nitrate-utilizing organisms and methanogens.
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