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Blom P, Smith GJ, van Kessel MAHJ, Koch H, Lücker S. Comprehensive evaluation of primer pairs targeting the ammonia monooxygenase subunit A gene of complete ammonia-oxidizing Nitrospira. Microbiol Spectr 2024; 12:e0051624. [PMID: 39166864 PMCID: PMC11448142 DOI: 10.1128/spectrum.00516-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 07/26/2024] [Indexed: 08/23/2024] Open
Abstract
Since the discovery of complete ammonia oxidizers (comammox) within the genus Nitrospira, their distribution and abundance across habitats have been intensively studied to better understand their ecological significance. Many primers targeting their ammonia monooxygenase subunit A gene (amoA) have been designed to detect and quantify comammox bacteria and to describe their community structure. We identified 38 published primers, but only few had high coverage and specificity for all known comammox Nitrospira or one of the two described subclades. For each target group, we comprehensively evaluated selected primer pairs using in silico analyses, endpoint PCRs, qPCRs, and amplicon sequencing on samples from various environments. Endpoint PCRs and qPCRs showed that the most commonly used primer pairs (comaA-244F/659R, comaB-244F/659R, and Ntsp-amoA162F/359R) produced several bands, which likely inflated quantifications via qPCR. In contrast, the recently published primer combinations CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R resulted mostly in a single band. Furthermore, amplicon sequencing demonstrated that these primer combinations also captured the highest richness of comammox Nitrospira. Taken together, our results indicate that few existing comammox amoA primer combinations have both high specificity and coverage and that the choice of these high-specificity and high-coverage primer pairs substantially impacts the accurate detection, quantification, and community description of comammox bacteria. We, therefore, recommend using the CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R primer pairs.IMPORTANCEBacteria that can fully convert ammonia via nitrite to nitrate, the complete ammonia oxidizers (comammox), were recently discovered and are found in many natural and engineered environments. PCR-based tools to study their abundance and diversity were rapidly developed, resulting in a plethora of primers available, many of which are widely used. The presence of comammox bacteria in an environment can, however, only be correctly determined if the used primers detect all members of this group while not detecting any other guilds. This study assesses the coverage and specificity of existing primers targeting comammox bacteria using both computational and standard molecular techniques, revealing large differences in their performance. The uniform usage of well-performing primers across studies could aid in generating comparable and generalizable data to better understand the importance of comammox bacteria in the environment.
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Affiliation(s)
- Pieter Blom
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Garrett J Smith
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Maartje A H J van Kessel
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Hanna Koch
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln an der Donau, Austria
| | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
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Li Z, Li D, Liu S, Zhao H, Li B, Shan S, Zhu Y, Sun J, Hou J. Impact of elevated CO 2 on microbial communities and functions in riparian sediments: Role of pollution levels in modulating effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176481. [PMID: 39341255 DOI: 10.1016/j.scitotenv.2024.176481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 08/14/2024] [Accepted: 09/21/2024] [Indexed: 09/30/2024]
Abstract
The impact of elevated CO2 levels on microorganisms is a focal point in studying the environmental effects of global climate change. A growing number of studies have demonstrated the importance of the direct effects of elevated CO2 on microorganisms, which are confounded by indirect effects that are not easily identified. Riparian zones have become key factor in identifying the environmental effects of global climate change because of their special location. However, the direct effects of elevated CO2 levels on microbial activity and function in riparian zone sediments remain unclear. In this study, three riparian sediments with different pollution risk levels of heavy metals and nutrients were selected to explore the direct response of microbial communities and functions to elevated CO2 excluding plants. The results showed that the short-term effects of elevated CO2 did not change the diversity of the bacterial and fungal communities, but altered the composition of their communities. Additionally, differences were observed in the responses of microbial functions to elevated CO2 levels among the three regions. Elevated CO2 promoted the activities of nitrification and denitrification enzymes and led to significant increases in N2O release in the three sediments, with the greatest increase of 76.09 % observed in the Yuyangshan Bay (YYS). Microbial carbon metabolism was promoted by elevated CO2 in YYS but was significantly inhibited by elevated CO2 in Gonghu Bay and Meiliang Bay. Moreover, TOC, TN, and Pb contents were identified as key factors contributing to the different microbial responses to elevated CO2 in sediments with different heavy metal and nutrient pollution. In conclusion, this study provides in-depth insights into the responses of bacteria and fungi in polluted riparian sediments to elevated CO2, which helps elucidate the complex interactions between microbial activity and environmental stressors.
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Affiliation(s)
- Ziyu Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Dapeng Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Songqi Liu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China.
| | - Huilin Zhao
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Boling Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Sujie Shan
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Yizhi Zhu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Jingqiu Sun
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Jun Hou
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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Abdulkader H, Gopal KS, Sasidharan S. Impact of floods and landslides on rhizosphere bacterial communities: a high-throughput 16S rRNA gene sequencing study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:56236-56252. [PMID: 39264494 DOI: 10.1007/s11356-024-34850-1] [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: 03/09/2024] [Accepted: 08/26/2024] [Indexed: 09/13/2024]
Abstract
This study investigates the diversity and composition of soil bacterial communities in the rhizosphere of Attapadi and Nelliyampathy, prominent hill stations in Palakkad district, Kerala, India. The persistent flooding and landslides in 2018 and 2019 significantly impacted agricultural productivity in these regions. Utilizing high-throughput 16S rRNA gene sequencing (Illumina MiSeq), we conducted a comprehensive analysis of soil samples. Correlative assessments between soil parameters and microbial relative abundance at the phylum level revealed noteworthy positive associations. Notably, nitrogen (N) exhibited a positive relation with Crenarchaeota, Chloroflexi, Actinobacteriota, and Acidobacteriota; pH correlated with Firmicutes; organic carbon (OC) with WPS-2; and phosphorous with Proteobacteria. A total of 31,402 operational taxonomic units (OTUs) were identified, with the highest feature counts observed in undisturbed soils from Attapadi (AUD) and Nelliyampathy (NUD) (13,007 and 12,915, respectively). Disturbed soils in Nelliyampathy (ND) and Attapadi (AD) displayed a substantial decline in microbial diversity and composition, harbouring 1409 and 4071 OTUs, respectively. Alpha and beta diversity indices further underscored the more severe impairment of ND soils compared to AD soils. Interestingly, a majority of ND samples were landslide-affected (four out of five), while flood-affected soils accounted for four out of six AD samples. This indicates that landslides exert a more pronounced impact on microbial diversity and composition than floods. The observed decline in microbial count, composition, and diversity, even after 2 years of the disaster, raises concerns about potential threats to agricultural output. The findings emphasize the need for corrective measures, including the incorporation of microbial inoculum, to restore soil fertility in post-disaster landscapes.
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Affiliation(s)
- Haseena Abdulkader
- Department of Agricultural Microbiology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, India.
| | - Kulkarni Surendra Gopal
- Department of Agricultural Microbiology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, India
| | - Sandeep Sasidharan
- Department of Soil Science, KSCSTE - Kerala Forest Research Institute, Peechi, Thrissur, Kerala, India
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Wang T, Gao M, Shao W, Wang L, Yang C, Wang X, Yao S, Zhang B. Dissecting the role of soybean rhizosphere-enriched bacterial taxa in modulating nitrogen-cycling functions. Appl Microbiol Biotechnol 2024; 108:347. [PMID: 38805033 PMCID: PMC11133221 DOI: 10.1007/s00253-024-13184-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Abstract
Crop roots selectively recruit certain microbial taxa that are essential for supporting their growth. Within the recruited microbes, some taxa are consistently enriched in the rhizosphere across various locations and crop genotypes, while others are unique to specific planting sites or genotypes. Whether these differentially enriched taxa are different in community composition and how they interact with nutrient cycling need further investigation. Here, we sampled bulk soil and the rhizosphere soil of five soybean varieties grown in Shijiazhuang and Xuzhou, categorized the rhizosphere-enriched microbes into shared, site-specific, and variety-specific taxa, and analyzed their correlation with the diazotrophic communities and microbial genes involved in nitrogen (N) cycling. The shared taxa were dominated by Actinobacteria and Thaumarchaeota, the site-specific taxa were dominated by Actinobacteria in Shijiazhuang and by Nitrospirae in Xuzhou, while the variety-specific taxa were more evenly distributed in several phyla and contained many rare operational taxonomic units (OTUs). The rhizosphere-enriched taxa correlated with most diazotroph orders negatively but with eight orders including Rhizobiales positively. Each group within the shared, site-specific, and variety-specific taxa negatively correlated with bacterial amoA and narG in Shijiazhuang and positively correlated with archaeal amoA in Xuzhou. These results revealed that the shared, site-specific, and variety-specific taxa are distinct in community compositions but similar in associations with rhizosphere N-cycling functions. They exhibited potential in regulating the soybean roots' selection for high-efficiency diazotrophs and the ammonia-oxidizing and denitrification processes. This study provides new insights into soybean rhizosphere-enriched microbes and their association with N cycling. KEY POINTS: • Soybean rhizosphere affected diazotroph community and enriched nifH, amoA, and nosZ. • Shared and site- and variety-specific taxa were dominated by different phyla. • Rhizosphere-enriched taxa were similarly associated with N-cycle functions.
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Affiliation(s)
- Tianshu Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Miao Gao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weiwei Shao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunyan Yang
- The Key Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050031, China
| | - Xing Wang
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, 221131, China
| | - Shuihong Yao
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Bin Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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Gao F, Li Y, Fan H, Luo D, Chapman SJ, Yao H. 15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils. Appl Microbiol Biotechnol 2024; 108:342. [PMID: 38789552 PMCID: PMC11126484 DOI: 10.1007/s00253-024-13170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/14/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15N-urea incubation has not been totally clarified. The 15N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C2H2 almost completely inhibited NO3--N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. KEY POINTS: • 15N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different.
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Affiliation(s)
- Fuyun Gao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, 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.
| | - Haoxin Fan
- 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
| | - Dan Luo
- College of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, 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.
- 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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6
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Tu X, Wang J, Liu X, Liu Y, Zhang Y, Uwiragiye Y, Elrys AS, Zhang J, Cai Z, Cheng Y, Müller C. Warming-Induced Stimulation of Soil N 2O Emissions Counteracted by Elevated CO 2 from Nine-Year Agroecosystem Temperature and Free Air Carbon Dioxide Enrichment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6215-6225. [PMID: 38546713 DOI: 10.1021/acs.est.3c10775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Globally, agricultural soils account for approximately one-third of anthropogenic emissions of the potent greenhouse gas and stratospheric ozone-depleting substance nitrous oxide (N2O). Emissions of N2O from agricultural soils are affected by a number of global change factors, such as elevated air temperatures and elevated atmospheric carbon dioxide (CO2). Yet, a mechanistic understanding of how these climatic factors affect N2O emissions in agricultural soils remains largely unresolved. Here, we investigate the soil N2O emission pathway using a 15N tracing approach in a nine-year field experiment using a combined temperature and free air carbon dioxide enrichment (T-FACE). We show that the effect of CO2 enrichment completely counteracts warming-induced stimulation of both nitrification- and denitrification-derived N2O emissions. The elevated CO2 induced decrease in pH and labile organic nitrogen (N) masked the stimulation of organic carbon and N by warming. Unexpectedly, both elevated CO2 and warming had little effect on the abundances of the nitrifying and denitrifying genes. Overall, our study confirms the importance of multifactorial experiments to understand N2O emission pathways from agricultural soils under climate change. This better understanding is a prerequisite for more accurate models and the development of effective options to combat climate change.
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Affiliation(s)
- Xiaoshun Tu
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Jing Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaoyu Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, and Center of Agricultural and Climate Change, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Liu
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Yinghua Zhang
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Yves Uwiragiye
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Department of Agriculture, Faculty of Agriculture, Environmental Management and Renewable Energy, University of Technology and Arts of Byumba, POB 25 Byumba, Rwanda
| | - Ahmed S Elrys
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
- Liebig Centre of Agroecology and Climate Impact Research, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Liebig Centre of Agroecology and Climate Impact Research, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Zucong Cai
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Yi Cheng
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Liebig Centre of Agroecology and Climate Impact Research, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
- Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing 210023, China
- Soil and Fertilizer & Resources and Environmental Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Christoph Müller
- Liebig Centre of Agroecology and Climate Impact Research, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
- Institute of Plant Ecology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield Dublin 4, Ireland
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Ghimire-Kafle S, Weaver ME, Kimbrel MP, Bollmann A. Competition between ammonia-oxidizing archaea and complete ammonia oxidizers from freshwater environments. Appl Environ Microbiol 2024; 90:e0169823. [PMID: 38349190 PMCID: PMC10952389 DOI: 10.1128/aem.01698-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/11/2024] [Indexed: 03/21/2024] Open
Abstract
Aerobic ammonia oxidizers (AOs) are prokaryotic microorganisms that contribute to the global nitrogen cycle by performing the first step of nitrification, the oxidation of ammonium to nitrite and nitrate. While aerobic AOs are found ubiquitously, their distribution is controlled by key environmental conditions such as substrate (ammonium) availability. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are generally found in oligotrophic environments with low ammonium availability. However, whether AOA and comammox share these habitats or outcompete each other is not well understood. We assessed the competition for ammonium between an AOA and comammox enriched from the freshwater Lake Burr Oak. The AOA enrichment culture (AOA-BO1) contained Nitrosarchaeum sp. BO1 as the ammonia oxidizer and Nitrospira sp. BO1 as the nitrite oxidizer. The comammox enrichment BO4 (cmx-BO4) contained the comammox strain Nitrospira sp. BO4. The competition experiments were performed either in continuous cultivation with ammonium as a growth-limiting substrate or in batch cultivation with initial ammonium concentrations of 50 and 500 µM. Regardless of the ammonium concentration, Nitrospira sp. BO4 outcompeted Nitrosarchaeum sp. BO1 under all tested conditions. The dominance of Nitrospira sp. BO4 could be explained by the ability of comammox to generate more energy through the complete oxidation of ammonia to nitrate and their more efficient carbon fixation pathway-the reductive tricarboxylic acid cycle. Our results are supported by the higher abundance of comammox compared to AOA in the sediment of Lake Burr Oak. IMPORTANCE Nitrification is a key process in the global nitrogen cycle. Aerobic ammonia oxidizers play a central role in the nitrogen cycle by performing the first step of nitrification. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are the dominant nitrifiers in environments with low ammonium availability. While AOA have been studied for almost 20 years, comammox were only discovered 8 years ago. Until now, there has been a gap in our understanding of whether AOA and comammox can co-exist or if one strain would be dominant under ammonium-limiting conditions. Here, we present the first study characterizing the competition between freshwater AOA and comammox under varying substrate concentrations. Our results will help in elucidating the niches of two key nitrifiers in freshwater lakes.
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Affiliation(s)
| | - Matt E. Weaver
- Department of Microbiology, Miami University, Oxford, Ohio, USA
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Meidl P, Lehmann A, Bi M, Breitenreiter C, Benkrama J, Li E, Riedo J, Rillig MC. Combined application of up to ten pesticides decreases key soil processes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:11995-12004. [PMID: 38227255 PMCID: PMC11289034 DOI: 10.1007/s11356-024-31836-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/29/2023] [Indexed: 01/17/2024]
Abstract
Natural systems are under increasing pressure by a range of anthropogenic global change factors. Pesticides represent a nearly ubiquitously occurring global change factor and have the potential to affect soil functions. Currently the use of synthetic pesticides is at an all-time high with over 400 active ingredients being utilized in the EU alone, with dozens of these pesticides occurring concurrently in soil. However, we presently do not understand the impacts of the potential interaction of multiple pesticides when applied simultaneously. Using soil collected from a local grassland, we utilize soil microcosms to examine the role of both rate of change and number of a selection of ten currently used pesticides on soil processes, including litter decomposition, water stable aggregates, aggregate size, soil pH, and EC. Additionally, we used null models to enrich our analyses to examine potential patterns caused by interactions between pesticide treatments. We find that both gradual and abrupt pesticide application have negative consequences for soil processes. Notably, pesticide number plays a significant role in affecting soil health. Null models also reveal potential synergistic behavior between pesticides which can further their consequences on soil processes. Our research highlights the complex impacts of pesticides, and the need for environmental policy to address the threats posed by pesticides.
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Affiliation(s)
- Peter Meidl
- Institut Für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Anika Lehmann
- Institut Für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Mohan Bi
- Institut Für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Carla Breitenreiter
- Institut Für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Jasmina Benkrama
- Institut Für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Erqin Li
- Institut Für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Judith Riedo
- Institut Für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Matthias C Rillig
- Institut Für Biologie, Freie Universität Berlin, Berlin, Germany.
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.
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9
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Pold G, Bonilla-Rosso G, Saghaï A, Strous M, Jones CM, Hallin S. Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles. ISME COMMUNICATIONS 2024; 4:ycae020. [PMID: 38584645 PMCID: PMC10999283 DOI: 10.1093/ismeco/ycae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 04/09/2024]
Abstract
The two evolutionarily unrelated nitric oxide-producing nitrite reductases, NirK and NirS, are best known for their redundant role in denitrification. They are also often found in organisms that do not perform denitrification. To assess the functional roles of the two enzymes and to address the sequence and structural variation within each, we reconstructed robust phylogenies of both proteins with sequences recovered from 6973 isolate and metagenome-assembled genomes and identified 32 well-supported clades of structurally distinct protein lineages. We then inferred the potential niche of each clade by considering other functional genes of the organisms carrying them as well as the relative abundances of each nir gene in 4082 environmental metagenomes across diverse aquatic, terrestrial, host-associated, and engineered biomes. We demonstrate that Nir phylogenies recapitulate ecology distinctly from the corresponding organismal phylogeny. While some clades of the nitrite reductase were equally prevalent across biomes, others had more restricted ranges. Nitrifiers make up a sizeable proportion of the nitrite-reducing community, especially for NirK in marine waters and dry soils. Furthermore, the two reductases showed distinct associations with genes involved in oxidizing and reducing other compounds, indicating that the NirS and NirK activities may be linked to different elemental cycles. Accordingly, the relative abundance and diversity of NirS versus NirK vary between biomes. Our results show the divergent ecological roles NirK and NirS-encoding organisms may play in the environment and provide a phylogenetic framework to distinguish the traits associated with organisms encoding the different lineages of nitrite reductases.
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Affiliation(s)
- Grace Pold
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Germán Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Marc Strous
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Christopher M Jones
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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10
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He H, Zhou J, Wang Y, Jiao S, Qian X, Liu Y, Liu J, Chen J, Delgado-Baquerizo M, Brangarí AC, Chen L, Cui Y, Pan H, Tian R, Liang Y, Tan W, Ochoa-Hueso R, Fang L. Deciphering microbiomes dozens of meters under our feet and their edaphoclimatic and spatial drivers. GLOBAL CHANGE BIOLOGY 2024; 30:e17028. [PMID: 37955302 DOI: 10.1111/gcb.17028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to be relatively stable and highly independent from climatic conditions. Much less is known, however, on how these microbial communities vary along climate gradients. Here, we used amplicon sequencing to investigate bacteria, archaea, and fungi along fifteen 18-m depth profiles at 20-50-cm intervals across contrasting aridity conditions in semi-arid forest ecosystems of China's Loess Plateau. Our results showed that bacterial and fungal α diversity and bacterial and archaeal community similarity declined dramatically in topsoil and remained relatively stable in deep soil. Nevertheless, deep soil microbiome still showed the functional potential of N cycling, plant-derived organic matter degradation, resource exchange, and water coordination. The deep soil microbiome had closer taxa-taxa and bacteria-fungi associations and more influence of dispersal limitation than topsoil microbiome. Geographic distance was more influential in deep soil bacteria and archaea than in topsoil. We further showed that aridity was negatively correlated with deep-soil archaeal and fungal richness, archaeal community similarity, relative abundance of plant saprotroph, and bacteria-fungi associations, but increased the relative abundance of aerobic ammonia oxidation, manganese oxidation, and arbuscular mycorrhizal in the deep soils. Root depth, complexity, soil volumetric moisture, and clay play bridging roles in the indirect effects of aridity on microbes in deep soils. Our work indicates that, even microbial communities and nutrient cycling in deep soil are susceptible to changes in water availability, with consequences for understanding the sustainability of dryland ecosystems and the whole-soil in response to aridification. Moreover, we propose that neglecting soil depth may underestimate the role of soil moisture in dryland ecosystems under future climate scenarios.
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Affiliation(s)
- Haoran He
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Jingxiong Zhou
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Yunqiang Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Earth and Environmental Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
| | - Yurong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Ji Liu
- Hubei Province Key Laboratory for Geographical Process Analysis and Simulation, Central China Normal University, Wuhan, China
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Albert C Brangarí
- Institute for Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Li Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongxing Cui
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Haibo Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Renmao Tian
- Institute for Food Safety and Health (IFSH), Illinois Institute of Technology, Bedford Park, Illinois, USA
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wenfeng Tan
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Raúl Ochoa-Hueso
- Department of Biology, IVAGRO, University of Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Campus del Rio San Pedro, Cádiz, Spain
| | - Linchuan Fang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Green Utilization of Critical Non-Metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan, China
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11
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Ranheim Sveen T, Hannula SE, Bahram M. Microbial regulation of feedbacks to ecosystem change. Trends Microbiol 2024; 32:68-78. [PMID: 37500365 DOI: 10.1016/j.tim.2023.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/29/2023]
Abstract
Microbes are key biodiversity components of all ecosystems and control vital ecosystem functions. Although we have just begun to unravel the scales and factors that regulate microbial communities, their role in mediating ecosystem stability in response to disturbances remains underexplored. Here, we review evidence of how, when, and where microbes regulate or drive disturbance feedbacks. Negative feedbacks dampen the impacts of disturbance, which maintain ecosystem stability, whereas positive feedbacks instead erode stability by amplifying the disturbance. Here we describe the processes underlying the responses to disturbance using a hierarchy of functional traits, and we exemplify how these may drive biogeochemical feedbacks. We suggest that the feedback potential of functional traits at different hierarchical levels is contingent on the complexity and heterogeneity of the environment.
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Affiliation(s)
- T Ranheim Sveen
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51 Uppsala, Sweden.
| | - S E Hannula
- Institute of Environmental Sciences, Leiden University, Leiden 2333, The Netherlands
| | - M Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51 Uppsala, Sweden; Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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12
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Bhardwaj L, Reddy B, Dubey SK. Deciphering insights into rhizospheric microbial community and soil parameters under the influence of herbicides in zero-tillage tropical rice-agroecosystem. ENVIRONMENTAL RESEARCH 2023; 237:117033. [PMID: 37660873 DOI: 10.1016/j.envres.2023.117033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
Extensive use of chemicals like herbicides in rice and other fields to manage weeds is expected to have a lasting influence on the soil environment. Considering this rationale, we aimed to decipher the effects of herbicides, Pendimethalin and Pretilachlor, applied at 0.5 and 0.6 kg ha-1, respectively on the rhizosphere microbial community and soil characteristics in the tropical rice field, managed under zero tillage cultivation. The quantity of herbicide residues declined gradually since application up to 60 days thereafter it reached the non-detectable level. Most of the soil variables viz., microbial biomass, soil enzymes etc., exhibited slight reduction in the treated soils compared to the control. A gradual decline was observed in Mineral-N, MBC, MBN and enzyme activities. Quantitative polymerase chain reaction results showed maximal microbial abundance of bacteria, fungi and archaea at mid-flowering stage of rice crop. The 16 rRNA and ITS region targeted amplicons high throughput sequencing microbial metagenomic approach revealed total of 94, 1353, and 510 species for archaea, bacteria and fungi, respectively. The metabarcoding of core microbiota revealed that the archaea comprised of Nitrososphaera, Nitrosocosmicus, and Methanosarcina. In the bacterial core microbiome, Neobacillus, Nitrospira, Thaurea, and Microvigra were found as the predominant taxa. Fusarium, Clonostachys, Nigrospora, Mortierella, Chaetomium, etc., were found in core fungal microbiome. Overall, the study exhibited that the recommended dose of herbicides found to be detrimental to the microbial dynamics, though a negative relation between residues and soil variables was observed that might alter the microbial diversity. The outcomes offer a comprehensive understanding of how herbicides affect the microbial community in zero tillage rice soil, thus has a critical imputation for eco-friendly and sustainable rice agriculture. Further, the long-term studies will be helpful in elucidating the role of identified microbial groups in sustaining the soil fertility and crop productivity.
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Affiliation(s)
- Laliteshwari Bhardwaj
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Bhaskar Reddy
- Virus Research and Diagnostic Laboratory, Government Institute of Medical Sciences, Greater Noida, Uttar Pradesh-9, 201310, India
| | - Suresh Kumar Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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13
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Zaman T, Asad SA, Irshad M, Faridullah, Shahzad M, Nazir R, Arefeen A, Iqbal A, Hafeez F. Unraveling the impact of human perturbation on nitrogen cycling in terrestrial ecosystems of lower Himalaya, Pakistan. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1324. [PMID: 37845391 DOI: 10.1007/s10661-023-11964-6] [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: 07/10/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023]
Abstract
Terrestrial ecosystems are under the enormous pressure of land use management regimes through human disturbances, resulting in the disruption of biogeochemical cycles and associated ecosystem services. Nitrogen (N) in soil ecosystems is of vital importance for primary productivity, hence estimating the extent of these human interventions on N-cycling processes becomes imperative from economic and environmental perspectives. This work investigated the impacts of variable anthropogenic activities on N cycling in three different terrestrial ecosystems (arable, grassland, and forest) in three regions of lower Himalaya, Pakistan. Potential nitrification (PNA) and denitrification (DEA) enzyme activities, relative distribution of inorganic N species (NH4, NO3), and the role of inherent edaphic factors were assessed. Results revealed high nitrification potentials and increased nitrous oxide (N2O) emissions in the incubated soil microcosms, in the order as arable > grassland > forest ecosystems. Notably, higher rates of both studied processes (~ 30-50%) and elevated soil mineral nitrogen pool were observed in arable ecosystems. Forest soils, assumed as pristine ecosystems relying mainly on natural N fixation, produced (de)nitrification rates relatively lower than grasslands, followed by arable soils which were moderately disturbed through long-term fertilization and intensive land-use regimes. Linear regression modeling revealed that the inorganic N species (particularly NO3), and inherent edaphic factors were the key determinants of high (de)nitrification rates, hence warn of accelerated N losses in these ecosystems. The study highlights that elevated PNA and DEA being proxies for the altered N cycling in the studied terrestrial ecosystems are of great ecological relevance in view of predicted N2O budget in the lower Himalaya.
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Affiliation(s)
- Tahir Zaman
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Saeed Ahmad Asad
- Department of Bio Sciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Muhammad Irshad
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Faridullah
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Muhammad Shahzad
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Rashid Nazir
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Awais Arefeen
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan
| | - Akhtar Iqbal
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan.
| | - Farhan Hafeez
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Tobe Camp University Road, Abbottabad, 22060, Pakistan.
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14
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Metze D, Schnecker J, Canarini A, Fuchslueger L, Koch BJ, Stone BW, Hungate BA, Hausmann B, Schmidt H, Schaumberger A, Bahn M, Kaiser C, Richter A. Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions. Nat Commun 2023; 14:5895. [PMID: 37736743 PMCID: PMC10516970 DOI: 10.1038/s41467-023-41524-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed 'vapor-qSIP') to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.
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Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alberto Canarini
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Benjamin J Koch
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Schaumberger
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Irdning, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria.
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15
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Jáuregui I, Vega-Mas I, Delaplace P, Vanderschuren H, Thonar C. An optimized hydroponic pipeline for large-scale identification of wheat genotypes with resilient biological nitrification inhibition activity. THE NEW PHYTOLOGIST 2023; 238:1711-1721. [PMID: 36764923 DOI: 10.1111/nph.18807] [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: 09/05/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Several plant species have been reported to inhibit nitrification via their root exudates, the so-called biological nitrification inhibition (BNI). Given the potential of BNI-producing plants to sustainably mitigate N losses in agrosystems, identification of BNI activity in existing germplasms is of paramount importance. A hydroponic system was combined with an optimized Nitrosomonas europaea-based bioassay to determine the BNI activity of root exudates. The pipeline allows collecting and processing hundreds of root exudates simultaneously. An additional assay was established to assess the potential bactericide effect of the root exudates. The pipeline was used to unravel the impact of developmental stage, temperature and osmotic stress on the BNI trait in selected wheat genotypes. Biological nitrification inhibition activity appeared consistently higher in wheat at the pretillering stage as compared to the tillering stage. While low-temperatures did not alter BNI activities in root exudates, osmotic stress appeared to change the BNI activity in a genotype-dependent manner. Further analysis of Nitrosomonas culture after pre-exposure to root exudates suggested that BNI activity has no or limited bactericide effects. The present pipeline will be instrumental to further investigating the dynamics of BNI activity and to uncover the diversity of the BNI trait in plant species.
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Affiliation(s)
- Iván Jáuregui
- Plant Genetics and Rhizosphere Processes laboratory, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, B-5030, Gembloux, Belgium
| | - Izargi Vega-Mas
- Plant Genetics and Rhizosphere Processes laboratory, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, B-5030, Gembloux, Belgium
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), 48940, Bilbao, Spain
| | - Pierre Delaplace
- Plant Genetics and Rhizosphere Processes laboratory, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, B-5030, Gembloux, Belgium
| | - Hervé Vanderschuren
- Plant Genetics and Rhizosphere Processes laboratory, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, B-5030, Gembloux, Belgium
- Tropical Crop Improvement Laboratory, Biosystems Department, KU Leuven, B-3001, Leuven, Belgium
| | - Cécile Thonar
- Plant Genetics and Rhizosphere Processes laboratory, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, B-5030, Gembloux, Belgium
- Agroecology Lab, Université Libre de Bruxelles (ULB), B-1050, Brussels, Belgium
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16
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Jiang Z, Tang S, Liao Y, Li S, Wang S, Zhu X, Ji G. Effect of low temperature on contributions of ammonia oxidizing archaea and bacteria to nitrous oxide in constructed wetlands. CHEMOSPHERE 2023; 313:137585. [PMID: 36529166 DOI: 10.1016/j.chemosphere.2022.137585] [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: 07/15/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Constructed wetlands (CWs) have been widely used for ecological remediation of micro-polluted source water. Nitrous oxide (N2O) from CWs has caused great concern as a greenhouse gas. However, the contribution of ammonia oxidation driven by ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) to N2O emission, especially at low temperature, was unknown. This study aimed to quantify the contributions of AOA and AOB to N2O through lab-scale subsurface CWs. The N2O emission flux of CW at 8 °C was 1.23 mg m-2·h-1, significantly lower than that at 25 °C (1.92 mg m-2·h-1). The contribution of ammonia oxidation to N2O at 8 °C (33.04%) was significantly higher than that at 25 °C (24.17%). The N2O production from AOA increased from 1.91 ng N·g-1 at 25 °C to 4.11 ng N·g-1 soil at 8 °C and its contribution increased from 23.38% to 30.18% (P < 0.05). Low temperature impaired functional gene groups and inhibited the activity of AOB, resulting in its declined contribution. Based on the transcriptional analysis, AOA was less affected by low temperature, thus stably contributing to N2O. Moreover, community diversity and relationships of AOA were enhanced at 8 °C, while AOB declined. The results confirmed the significant contribution of AOA and demonstrated molecular mechanisms (higher activity and community stability) of the increased contribution of AOA to N2O at low temperature.
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Affiliation(s)
- Zhuo Jiang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Shuangyu Tang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Yinhao Liao
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Shuo Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Xianfang Zhu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China.
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17
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Liao J, Luo Q, Hu A, Wan W, Tian D, Ma J, Ma T, Luo H, Lu S. Soil moisture-atmosphere feedback dominates land N 2 O nitrification emissions and denitrification reduction. GLOBAL CHANGE BIOLOGY 2022; 28:6404-6418. [PMID: 35971257 DOI: 10.1111/gcb.16365] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Soil moisture (SM) is essential to microbial nitrogen (N)-cycling networks in terrestrial ecosystems. Studies have found that SM-atmosphere feedbacks dominate the changes in land carbon fluxes. However, the influence of SM-atmosphere feedbacks on the N fluxes changes, and the underlying mechanisms remain highly unsure, leading to uncertainties in climate projections. To fill this gap, we used in situ observation coupled with gridded and remote sensing data to analyze N2 O fluxes emissions globally. Here, we investigated the synergistic effects of temperature, hydroclimate on global N2 O fluxes, as the result of SM-atmosphere feedback impact on N fluxes. We found that SM-temperature feedback dominates land N2 O emissions by controlling the balance between nitrifier and denitrifier genes. The mechanism is that atmospheric water demand increases with temperature and thereby reduces SM, which increases the dominant N2 O production nitrifier (containing amoA AOB gene) and decreases the N2 O consumption denitrifier (containing the nosZ gene), consequently will potential increasing N2 O emissions. However, we find that the spatial variations of soil-water availability as a result of the nonlinear response of SM to vapor pressure deficit caused by temperature are some of the greatest challenges in predicting future N2 O emissions. Our data-driven assessment deepens the understanding of the impact of SM-atmosphere interactions on the soil N cycle, which remains uncertain in earth system models. We suggest that the model needs to account for feedback between SM and atmospheric temperature when estimating the response of the N2 O emissions to climatic change globally, as well as when conducting field-scale investigations of the response of the ecosystem to warming.
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Affiliation(s)
- Jiayuan Liao
- Key Laboratory of Soil and Water Conservation and Desertification Combating in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China
- School of Atmospheric Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Qiqi Luo
- School of Atmospheric Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Ang Hu
- College of Resources and Environment, Hunan Agricultural University, Changsha, China
| | - Wenkai Wan
- Key Laboratory of Soil and Water Conservation and Desertification Combating in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Dian Tian
- Key Laboratory of Soil and Water Conservation and Desertification Combating in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Jingwei Ma
- Key Laboratory of Soil and Water Conservation and Desertification Combating in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Tian Ma
- School of Atmospheric Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Hao Luo
- School of Atmospheric Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Sheng Lu
- Key Laboratory of Soil and Water Conservation and Desertification Combating in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China
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18
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Yue H, Banerjee S, Liu C, Ren Q, Zhang W, Zhang B, Tian X, Wei G, Shu D. Fertilizing-induced changes in the nitrifying microbiota associated with soil nitrification and crop yield. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 841:156752. [PMID: 35718181 DOI: 10.1016/j.scitotenv.2022.156752] [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: 02/23/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Ammonia oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira (CMX) play pivotal roles in global nitrogen-cycling network. Despite its importance, the driving forces for niche specialization of these nitrifiers, as well as their relative contributions to nitrification and crop yield have not been fully understood. Here, we investigated the niche specialization and environmental prevalence of nitrifying communities, and their importance for the nitrification rate and crop yield across a gradient of nitrogen inputs in a two-decade old field experiment. The results of 15N-tracer and quantitative PCR revealed that AOB and NOB jointly determined the gross nitrification rates across mineral fertilizer treatments, whereas AOA and AOB contributed more than other nitrifiers to nitrification under with organic fertilizer amendments. Linear regression model revealed that crop yield could be linked with AOB and NOB under inorganic farming but closely associated with CMX under organic management. Amplicon sequencing of these functional genes further demonstrated that mineral and organic fertilizers have distinct influences on the β-diversity and niche breadth of these nitrifying communities, indicating that fertilization triggered niche specialization of nitrifying guilds in agricultural soils. Notably, organic fertilization enhanced the network complexity of these nitrifiers by harboring keystone taxa. Random forest analysis provide robustly evidence for the hypothesis that abundance of functional genes contributed more than a- and β-diversity of these nitrifiers for driving nitrification rates and crop yields. Collectively, these findings provide the empirical evidence for the environmental adaptation and niche specialization of nitrifying communities, and their contributions in nitrification and crop yield when confronted with long-term nitrogen inputs.
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Affiliation(s)
- Hong Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo 58102, ND, USA
| | - Conghui Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiyong Ren
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wu Zhang
- Heihe Branch, Heilongjiang Academy of Agricultural Sciences, Heihe, Heilongjiang 150086, China
| | - Baogang Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaohong Tian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Duntao Shu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
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19
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Tu X, Wang J, Liu X, Elrys AS, Cheng Y, Zhang J, Cai ZC, Müller C. Inhibition of Elevated Atmospheric Carbon Dioxide to Soil Gross Nitrogen Mineralization Aggravated by Warming in an Agroecosystem. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:12745-12754. [PMID: 35985002 DOI: 10.1021/acs.est.2c04378] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The response of soil gross nitrogen (N) cycling to elevated carbon dioxide (CO2) concentration and temperature has been extensively studied in natural and semi-natural ecosystems. However, how these factors and their interaction affect soil gross N dynamics in agroecosystems, strongly disturbed by human activity, remains largely unknown. Here, a 15N tracer study under aerobic incubation was conducted to quantify soil gross N transformation rates in a paddy field exposed to elevated CO2 and/or temperature for 9 years in a warming and free air CO2 enrichment experiment. Results show that long-term exposure to elevated CO2 significantly inhibited or tended to inhibit gross N mineralization at elevated and ambient temperatures, respectively. The inhibition of soil gross N mineralization by elevating CO2 was aggravated by warming in this paddy field. The inhibition of gross N mineralization under elevated CO2 could be due to decreased soil pH. Long-term exposure to elevated CO2 also significantly reduced gross autotrophic nitrification at ambient temperature, probably due to decreased soil pH and gross N mineralization. In contrast, none of the gross N transformation rates were affected by long-term exposure to warming alone. Our study provides strong evidence that long-term dual exposure to elevated CO2 and temperature has a greater negative effect on gross N mineralization rate than the single exposure, potentially resulting in progressive N limitation in this agroecosystem and ultimately increasing demand for N fertilizer.
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Affiliation(s)
- Xiaoshun Tu
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Jing Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaoyu Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, and Center of Agricultural and Climate Change, Nanjing Agricultural University, Nanjing 210095, China
| | - Ahmed S Elrys
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Yi Cheng
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
- Ministry of Education, Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Nanjing 210023, China
| | - Jinbo Zhang
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Zu-Cong Cai
- School of Geography, Nanjing Normal University, Nanjing 210023, China
| | - Christoph Müller
- Institute of Plant Ecology, Justus Liebig University Giessen, Giessen 35392, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin D04, Ireland
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20
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Climate change did not alter the effects of Bt maize on soil Collembola in northeast China. Sci Rep 2022; 12:13435. [PMID: 35927281 PMCID: PMC9352747 DOI: 10.1038/s41598-022-16783-2] [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: 10/20/2021] [Accepted: 07/15/2022] [Indexed: 11/17/2022] Open
Abstract
Bt maize is being increasingly cultivated worldwide as the effects of climate change are increasing globally. Bt maize IE09S034 and its near-isogenic non-Bt maize Zong 31 were used to investigate whether climate change alters the effects of Bt maize on soil Collembola. Warming and drought conditions were simulated using open-top chambers (OTC), and their effects on soil Collembola were evaluated. We found that the maize type had no significant effect on Collembola; however, the abundance and diversity of Collembola were significantly higher in the OTC than outside at the seedling stage; they were significantly lower in the OTC at the heading and mature stages. The interactions of the maize type with the OTC had no effect on these parameters. Therefore, Bt maize had no significant effect on soil Collembola, and the effects of climate warming and drought on soil Collembola depended on the ambient climatic conditions. When the temperature was low, collembolan abundance and diversity were promoted by warming; however, when the temperature was high and the humidity was low, collembolan abundance and diversity were inhibited by warming and drought. The climate changes simulated by the OTC did not alter the effects of Bt maize on soil Collembola.
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21
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Wu D, Deng L, Sun Y, Wang R, Zhang L, Wang R, Song Y, Gao Z, Haider H, Wang Y, Hou L, Liu M. Climate warming, but not Spartina alterniflora invasion, enhances wetland soil HONO and NO x emissions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153710. [PMID: 35149064 DOI: 10.1016/j.scitotenv.2022.153710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/27/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Climate warming and invasive plant growth (plant invasion) may aggravate air pollution by affecting soil nitrogen (N) cycling and the emissions of reactive N gases, such as nitrous acid (HONO) and nitrogen oxides (NOx). However, little is known about the response of soil NOy (HONO + NOx) emissions and microbial functional genes to the interaction of climate warming and plant invasion. Here, we found that experimental warming (approximately 1.5 °C), but not Spartina alterniflora invasion, increased NOy emissions (0-140 ng N m-2 s-1) of treated wetland soils by 4-10 fold. Warming also decreased soil archaeal and fungal richness and diversity, shifted their community structure (e.g., decreased the archaeal classes Thermoplasmata and Iainarchaeia, and increased the archaeal genus Candidatus Nitrosoarchaeum, and the fungal classes Saccharomycetes and Tritirachiomycetes), and decreased the overall abundance of soil N cycling genes. Structural equation modeling revealed that warming-associated changes in edaphic factors and the microbial N cycling potential are responsible for the observed increase in soil NOy emissions. Collectively, the results showed that climate warming accelerates soil N cycling by stimulating large soil HONO and NOx emissions, and influences air quality by contributing to atmospheric reactive N and ozone cycling.
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Affiliation(s)
- Dianming Wu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 200241 Shanghai, China; Institute of Eco-Chongming (IEC), 202162 Shanghai, China.
| | - Lingling Deng
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 200241 Shanghai, China
| | - Yihua Sun
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060 Shenzhen, China
| | - Ruhai Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of soil Sciences, Chinese Academy of Sciences, 210008 Nanjing, China
| | - Li Zhang
- School of Resources and Environment, Anhui Agricultural University, 230036 Hefei, China
| | - Rui Wang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 200241 Shanghai, China
| | - Yaqi Song
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 200241 Shanghai, China; College of Biology and the Environment, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, 210037 Nanjing, China
| | - Zhiwei Gao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 200241 Shanghai, China
| | - Haroon Haider
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 200241 Shanghai, China
| | - Yue Wang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 200241 Shanghai, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 200241 Shanghai, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 200241 Shanghai, China; Institute of Eco-Chongming (IEC), 202162 Shanghai, China
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22
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Zhong Y, Liu J, Jia X, Tang Z, Shangguan Z, Wang R, Yan W. Environmental stress-discriminatory taxa are associated with high C and N cycling functional potentials in dryland grasslands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:152991. [PMID: 35026259 DOI: 10.1016/j.scitotenv.2022.152991] [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: 08/31/2021] [Revised: 12/03/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Increasing environmental stress strongly affects soil microbial communities, but the responses of the microbial assembly and the functional potential of the dominant microbial community in the presence of environmental stress in drylands are still poorly understood. Here, we undertook a broad appraisal of the abundance, diversity, similarity, community assembly, network properties and functions of soil microbiomes in 82 dryland grasslands along environmental gradients. We found that the bacterial and fungal diversity and community similarity showed different sensitivities to environmental stress (decreased mean annual precipitation (MAP) and soil nutrient levels and increased soil pH), and MAP was the most important factor influencing microbial community patterns. In addition, the dominant subcommunity of both bacteria and fungi was more sensitive to environmental stress than the nondominant subcommunity. Although increasing environmental stress decreased microbial phylogenetic clustering, it had no effects on the stochastic and deterministic assembly process balance. Moreover, we identified 101 bacterial and 34 fungal environmental stress-discriminatory taxa that were sensitive to environmental stress, and these bacterial markers showed a high correlation with the abundance of carbon (C) and nitrogen (N) cycling-related genes, whereas the taxa classified as connectors in the network were mainly correlated with C degradation genes. Our study shows that the different responses of bacteria and fungi to environmental stress bring challenges to predicting microbial function, but a relatively small number of taxa play an important role in driving C and N cycling-related functional genes, indicating that identifying an organism's phenotypic characteristics or traits of key taxa may improve our knowledge of the microbial response to ongoing global changes.
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Affiliation(s)
- Yangquanwei Zhong
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Jin Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xiaoyu Jia
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Zhuangsheng Tang
- College of Grassland Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem of the Ministry of Education, Lanzhou 730070, PR China
| | - Zhouping Shangguan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Institute of Soil and Water Conservation, Chinese Academy of Sciences, Yangling, Shaanxi 712100, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ruiwu Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Weiming Yan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Institute of Soil and Water Conservation, Chinese Academy of Sciences, Yangling, Shaanxi 712100, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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23
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Maxwell TL, Canarini A, Bogdanovic I, Böckle T, Martin V, Noll L, Prommer J, Séneca J, Simon E, Piepho HP, Herndl M, Pötsch EM, Kaiser C, Richter A, Bahn M, Wanek W. Contrasting drivers of belowground nitrogen cycling in a montane grassland exposed to a multifactorial global change experiment with elevated CO 2 , warming, and drought. GLOBAL CHANGE BIOLOGY 2022; 28:2425-2441. [PMID: 34908205 DOI: 10.5281/zenodo.5597021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/26/2021] [Accepted: 11/28/2021] [Indexed: 05/26/2023]
Abstract
Depolymerization of high-molecular weight organic nitrogen (N) represents the major bottleneck of soil N cycling and yet is poorly understood compared to the subsequent inorganic N processes. Given the importance of organic N cycling and the rise of global change, we investigated the responses of soil protein depolymerization and microbial amino acid consumption to increased temperature, elevated atmospheric CO2 , and drought. The study was conducted in a global change facility in a managed montane grassland in Austria, where elevated CO2 (eCO2 ) and elevated temperature (eT) were stimulated for 4 years, and were combined with a drought event. Gross protein depolymerization and microbial amino acid consumption rates (alongside with gross organic N mineralization and nitrification) were measured using 15 N isotope pool dilution techniques. Whereas eCO2 showed no individual effect, eT had distinct effects which were modulated by season, with a negative effect of eT on soil organic N process rates in spring, neutral effects in summer, and positive effects in fall. We attribute this to a combination of changes in substrate availability and seasonal temperature changes. Drought led to a doubling of organic N process rates, which returned to rates found under ambient conditions within 3 months after rewetting. Notably, we observed a shift in the control of soil protein depolymerization, from plant substrate controls under continuous environmental change drivers (eT and eCO2 ) to controls via microbial turnover and soil organic N availability under the pulse disturbance (drought). To the best of our knowledge, this is the first study which analyzed the individual versus combined effects of multiple global change factors and of seasonality on soil organic N processes and thereby strongly contributes to our understanding of terrestrial N cycling in a future world.
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Affiliation(s)
- Tania L Maxwell
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
- INRAE, Bordeaux Sciences Agro, ISPA, Villenave d'Ornon, France
| | - Alberto Canarini
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Ivana Bogdanovic
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Theresa Böckle
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Victoria Martin
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Lisa Noll
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Judith Prommer
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Joana Séneca
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Eva Simon
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Hans-Peter Piepho
- Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Markus Herndl
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Irdning-Donnersbachtal, Austria
| | - Erich M Pötsch
- Agricultural Research and Education Centre Raumberg-Gumpenstein, Irdning-Donnersbachtal, Austria
| | - Christina Kaiser
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Andreas Richter
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
| | - Michael Bahn
- Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Wolfgang Wanek
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Center of Microbiology and Environmental Systems Science, Vienna, Austria
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24
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Maxwell TL, Canarini A, Bogdanovic I, Böckle T, Martin V, Noll L, Prommer J, Séneca J, Simon E, Piepho H, Herndl M, Pötsch EM, Kaiser C, Richter A, Bahn M, Wanek W. Contrasting drivers of belowground nitrogen cycling in a montane grassland exposed to a multifactorial global change experiment with elevated CO 2 , warming, and drought. GLOBAL CHANGE BIOLOGY 2022; 28:2425-2441. [PMID: 34908205 PMCID: PMC9306501 DOI: 10.1111/gcb.16035] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/26/2021] [Accepted: 11/28/2021] [Indexed: 05/13/2023]
Abstract
Depolymerization of high-molecular weight organic nitrogen (N) represents the major bottleneck of soil N cycling and yet is poorly understood compared to the subsequent inorganic N processes. Given the importance of organic N cycling and the rise of global change, we investigated the responses of soil protein depolymerization and microbial amino acid consumption to increased temperature, elevated atmospheric CO2 , and drought. The study was conducted in a global change facility in a managed montane grassland in Austria, where elevated CO2 (eCO2 ) and elevated temperature (eT) were stimulated for 4 years, and were combined with a drought event. Gross protein depolymerization and microbial amino acid consumption rates (alongside with gross organic N mineralization and nitrification) were measured using 15 N isotope pool dilution techniques. Whereas eCO2 showed no individual effect, eT had distinct effects which were modulated by season, with a negative effect of eT on soil organic N process rates in spring, neutral effects in summer, and positive effects in fall. We attribute this to a combination of changes in substrate availability and seasonal temperature changes. Drought led to a doubling of organic N process rates, which returned to rates found under ambient conditions within 3 months after rewetting. Notably, we observed a shift in the control of soil protein depolymerization, from plant substrate controls under continuous environmental change drivers (eT and eCO2 ) to controls via microbial turnover and soil organic N availability under the pulse disturbance (drought). To the best of our knowledge, this is the first study which analyzed the individual versus combined effects of multiple global change factors and of seasonality on soil organic N processes and thereby strongly contributes to our understanding of terrestrial N cycling in a future world.
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Affiliation(s)
- Tania L. Maxwell
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
- INRAEBordeaux Sciences AgroISPAVillenave d'OrnonFrance
| | - Alberto Canarini
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Ivana Bogdanovic
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Theresa Böckle
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Victoria Martin
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Lisa Noll
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Judith Prommer
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Joana Séneca
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Eva Simon
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | | | - Markus Herndl
- Agricultural Research and Education Centre Raumberg‐GumpensteinIrdning‐DonnersbachtalAustria
| | - Erich M. Pötsch
- Agricultural Research and Education Centre Raumberg‐GumpensteinIrdning‐DonnersbachtalAustria
| | - Christina Kaiser
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Andreas Richter
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
| | - Michael Bahn
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Wolfgang Wanek
- Division of Terrestrial Ecosystem ResearchDepartment of Microbiology and Ecosystem ScienceCenter of Microbiology and Environmental Systems ScienceViennaAustria
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25
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Pan J, Liu Y, Yang Y, Cheng Z, Lan X, Hu W, Shi G, Zhang Q, Feng H. Slope aspect determines the abundance and composition of nitrogen-cycling microbial communities in an alpine ecosystem. Environ Microbiol 2022; 24:3598-3611. [PMID: 35048487 DOI: 10.1111/1462-2920.15900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 01/11/2022] [Indexed: 11/28/2022]
Abstract
Slope aspect is an important topographic feature that can influence local environmental conditions. While strong effects of slope aspect on aboveground and belowground communities have been frequently elucidated, how slope aspect affects soil nitrogen (N) cycling microbes remains unclear. Here, we characterized the communities of soil N-cycling microbes on south- and north-facing slopes in an alpine ecosystem, by quantifying (qPCR) and high-throughput sequencing six genes involved in N-fixation (nifH), nitrification (archaeal and bacterial amoA) and denitrification (nirK, nirS and nosZ). We found that the abundance, diversity and community composition of major N-cycling microbes differed dramatically between the two slope aspects, and these variances could be well explained by the aspect-driven differences in environmental conditions, especially soil temperature and moisture. The response patterns of different N-cycling groups to slope aspect were much inconsistent, especially for those with similar functions (i.e. ammonia-oxidizing archaea vs. bacteria, nirK- vs. nirS-reducers), indicating strong niche differentiation between these counterparts. We also observed strong preferences and distinct co-occurrence patterns of N-cycling microbial taxa for the two slope aspects. These findings highlight the importance of slope aspect in determining the abundance, species distribution and community structure of N-cycling microbes, and consequently influencing N-cycling processes and ecosystem functioning. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jianbin Pan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yongjun Liu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.,State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730000, China
| | - Yue Yang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zhongxia Cheng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaomei Lan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Weigang Hu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Guoxi Shi
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, 741000, China
| | - Qi Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Huyuan Feng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China
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26
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Zhang L, Chen M, Chen X, Wang J, Zhang Y, Xiao X, Hu C, Liu J, Zhang R, Xu D, Jiao N, Zhang Y. Nitrifiers drive successions of particulate organic matter and microbial community composition in a starved macrocosm. ENVIRONMENT INTERNATIONAL 2021; 157:106776. [PMID: 34311224 DOI: 10.1016/j.envint.2021.106776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Organic carbon produced by nitrifiers plays an important role in maintaining the microbial metabolism in the aphotic ocean layer with carbon and energy scarcity. However, the contribution of nitrifiers to organic carbon processing remains unclear. To explore how nitrification impacts the material cycle in the starved ecosystem, we set up an ultra-large volume, long-term incubation experiment. Seawater collected from the Halifax coastal ocean was pumped into the Aquatron Tower Tank located at Dalhousie University, Canada, and was incubated under dark conditions for 73 days. The results indicated that the relative abundance of nitrifiers increased and nitrification was strengthened in the dark system where energy and organic carbon were scarce. The importance of nitrogenous compounds in particulate materials increased over the course of the incubation. Correlation analysis showed that the relative abundances of nitrifiers and particulate organic compounds containing nitrogen were significantly and positively correlated. Furthermore, network analysis suggested that metabolic processes related to nitrogenous and aromatic compounds are most important to particle associated bacteria. This study suggests that the nitrifiers could produce a series of organic compounds that result in the alteration of organic matter composition by promoting the degradation of recalcitrant aromatic compounds, which has important implications for organic matter processing in the starved dark ecosystem.
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Affiliation(s)
- Lianbao Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Jianning Wang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Yu Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Xilin Xiao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Chen Hu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qinagdao 266237, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China.
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27
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Liang D, Robertson GP. Nitrification is a minor source of nitrous oxide (N 2 O) in an agricultural landscape and declines with increasing management intensity. GLOBAL CHANGE BIOLOGY 2021; 27:5599-5613. [PMID: 34383336 PMCID: PMC9291997 DOI: 10.1111/gcb.15833] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/16/2021] [Accepted: 07/30/2021] [Indexed: 05/15/2023]
Abstract
The long-term contribution of nitrification to nitrous oxide (N2 O) emissions from terrestrial ecosystems is poorly known and thus poorly constrained in biogeochemical models. Here, using Bayesian inference to couple 25 years of in situ N2 O flux measurements with site-specific Michaelis-Menten kinetics of nitrification-derived N2 O, we test the relative importance of nitrification-derived N2 O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest. We found that the maximum potential contribution from nitrification to in situ N2 O fluxes was 13%-17% in a conventionally fertilized annual cropping system, 27%-42% in a low-input cover-cropped annual cropping system, and 52%-63% in perennial systems including a late successional deciduous forest. Actual values are likely to be <10% of these values because of low N2 O yields in cultured nitrifiers (typically 0.04%-8% of NH3 oxidized) and competing sinks for available NH4+ in situ. Most nitrification-derived N2 O was produced by ammonia-oxidizing bacteria rather than archaea, who appeared responsible for no more than 30% of nitrification-derived N2 O production in all but one ecosystem. Although the proportion of nitrification-derived N2 O production was lowest in annual cropping systems, these ecosystems nevertheless produced more nitrification-derived N2 O (higher Vmax ) than perennial and successional ecosystems. We conclude that nitrification is minor relative to other sources of N2 O in all ecosystems examined.
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Affiliation(s)
- Di Liang
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
- W. K. Kellogg Biological StationMichigan State UniversityHickory CornersMichiganUSA
| | - G. Philip Robertson
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
- W. K. Kellogg Biological StationMichigan State UniversityHickory CornersMichiganUSA
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Wang H, Bagnoud A, Ponce-Toledo RI, Kerou M, Weil M, Schleper C, Urich T. Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils. mSystems 2021; 6:e0054621. [PMID: 34463572 DOI: 10.1128/msystems.00546-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/12/2021] [Indexed: 01/04/2023] Open
Abstract
A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase (amoA) was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations. However, many microbiome studies target the 16S rRNA gene as a marker; thus, the usage of this novel taxonomy is currently limited. Here, we exploited the phylogenetic congruence of archaeal amoA and 16S rRNA genes to link 16S rRNA gene classification to the novel amoA taxonomy. We screened publicly available archaeal genomes and contigs for the co-occurring amoA and 16S rRNA genes and constructed a 16S rRNA gene database with the corresponding amoA clade taxonomy. Phylogenetic trees of both marker genes confirmed congruence, enabling the identification of clades. We validated this approach with 16S rRNA gene amplicon data from peatland soils. We succeeded in linking 16S rRNA gene amplicon sequence variants belonging to the class Nitrososphaeria to seven different AOA (amoA) clades, including two of the most frequently detected clades (Nitrososphaerales γ and δ clades) for which no pure culture is currently available. Water status significantly impacted the distribution of the AOA clades as well as the whole AOA community structure, which was correlated with pH, nitrate, and ammonium, consistent with previous clade predictions. Our study emphasizes the need to distinguish among AOA clades with distinct ecophysiologies and environmental preferences, for a better understanding of the ecology of the globally abundant AOA. IMPORTANCE The recently established phylogeny of amoA provides a finer resolution than previous studies, allowing clustering of AOA beyond the order level and thus revealing novel clades. While the 16S rRNA gene is mostly appreciated in microbiome studies, this novel phylogeny is in limited use. Here, we provide an alternative path to identifying AOA with this novel and highly resolved amoA taxonomy by using 16S rRNA gene sequencing data. We constructed a 16S rRNA gene database with the associated amoA clade taxonomy based on their phylogenetic congruence. With this database, we were able to assign 16S rRNA gene amplicons from peatland soils to different AOA clades, with a level of resolution provided previously only by amoA phylogeny. As 16S rRNA gene amplicon sequencing is still widely employed in microbiome studies, our database may have a broad application for interpreting the ecology of globally abundant AOA.
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Affiliation(s)
- Haitao Wang
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
| | - Alexandre Bagnoud
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Rafael I Ponce-Toledo
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Melina Kerou
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Micha Weil
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, University of Viennagrid.10420.37, Vienna, Austria
| | - Tim Urich
- Institute of Microbiology, University of Greifswaldgrid.5603.0, Greifswald, Germany
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