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Kang P, Hu J, Pan Y, Qu X, Ran Y, Yang C, Liu B. Response of soil fungal-community structure and function to land conversion to agriculture in desert grassland. Front Microbiol 2024; 15:1413973. [PMID: 39318436 PMCID: PMC11420991 DOI: 10.3389/fmicb.2024.1413973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 08/06/2024] [Indexed: 09/26/2024] Open
Abstract
Land conversion to agriculture is an important factor affecting soil ecological processes in the desert grasslands of northern China. However, soil fungal-community structure and function in response to Land conversion remain unclear. In this study, desert grassland, artificial shrubland, and land conversion were investigated in the western part of the Mu Us Sandland (Yanchi, Ningxia; Dingbian, Shaanxi). We found that land conversion significantly increased soil total carbon, nitrogen, and phosphorus, and available phosphorous and potassium contents. In the early stage of conversion to agricultural (April), soil fungal operational taxonomic units and abundance-based coverage estimator were lower than those of dessert grasslands and shrubland plots and had significant correlations with pH, electric conductivity, and available phosphorus and potassium. The dominant phyla strongly correlated with soil physicochemical properties. Concomitantly, the relative abundance of Glomeromycota was significantly lower, and the complexity of the network in the land conversion plots was lower than that in the shrubland plots. In the late stage of land conversion (September), soil fungal operational taxonomic units and abundance-based coverage estimator were lower in the conversion plots than in the desert grassland plots, with more complex network relationships compared to the desert grassland or shrubland plots. Symbiotrophic groups, a functional group of desert grassland soil fungi, can be used as a predictor of environmental change; in addition, land conversion decreases the relative abundance of arbuscular mycorrhizal functional groups. Our study highlights the response of soil fungal communities and functions to human disturbances in desert grasslands. Considering the potential of land conversion to agriculture to influence soil secondary salinization, there is a need for continued observation of soil ecological health over the time continuum of land conversion to agriculture.
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Affiliation(s)
- Peng Kang
- School of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Jinpeng Hu
- School of Biological Science and Engineering, North Minzu University, Yinchuan, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yaqing Pan
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xuan Qu
- School of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Yichao Ran
- School of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Chenxi Yang
- School of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Bingru Liu
- School of Biological Science and Engineering, North Minzu University, Yinchuan, China
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2
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Abdoli P, Vulin C, Lepiz M, Chase AB, Weihe C, Rodríguez-Verdugo A. Substrate complexity buffers negative interactions in a synthetic community of leaf litter degraders. FEMS Microbiol Ecol 2024; 100:fiae102. [PMID: 39020097 PMCID: PMC11289631 DOI: 10.1093/femsec/fiae102] [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: 01/13/2024] [Revised: 07/02/2024] [Accepted: 07/16/2024] [Indexed: 07/19/2024] Open
Abstract
Leaf litter microbes collectively degrade plant polysaccharides, influencing land-atmosphere carbon exchange. An open question is how substrate complexity-defined as the structure of the saccharide and the amount of external processing by extracellular enzymes-influences species interactions. We tested the hypothesis that monosaccharides (i.e. xylose) promote negative interactions through resource competition, and polysaccharides (i.e. xylan) promote neutral or positive interactions through resource partitioning or synergism among extracellular enzymes. We assembled a three-species community of leaf litter-degrading bacteria isolated from a grassland site in Southern California. In the polysaccharide xylan, pairs of species stably coexisted and grew equally in coculture and in monoculture. Conversely, in the monosaccharide xylose, competitive exclusion and negative interactions prevailed. These pairwise dynamics remained consistent in a three-species community: all three species coexisted in xylan, while only two species coexisted in xylose, with one species capable of using peptone. A mathematical model showed that in xylose these dynamics could be explained by resource competition. Instead, the model could not predict the coexistence patterns in xylan, suggesting other interactions exist during biopolymer degradation. Overall, our study shows that substrate complexity influences species interactions and patterns of coexistence in a synthetic microbial community of leaf litter degraders.
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Affiliation(s)
- Parmis Abdoli
- Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA 92697, United States
| | - Clément Vulin
- Department of Fundamental Microbiology, University of Lausanne, Biophore, CH-1015 Lausanne, Switzerland
| | - Miriam Lepiz
- Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA 92697, United States
| | - Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, 3225 Daniel Avenue, Suite 207, Heroy Hall, Dallas, TX 75205, United States
| | - Claudia Weihe
- Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA 92697, United States
| | - Alejandra Rodríguez-Verdugo
- Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA 92697, United States
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3
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Li S, Delgado-Baquerizo M, Ding J, Hu H, Huang W, Sun Y, Ni H, Kuang Y, Yuan MM, Zhou J, Zhang J, Liang Y. Intrinsic microbial temperature sensitivity and soil organic carbon decomposition in response to climate change. GLOBAL CHANGE BIOLOGY 2024; 30:e17395. [PMID: 38923190 DOI: 10.1111/gcb.17395] [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: 12/30/2023] [Revised: 05/23/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Soil microbes are essential for regulating carbon stocks under climate change. However, the uncertainty surrounding how microbial temperature responses control carbon losses under warming conditions highlights a significant gap in our climate change models. To address this issue, we conducted a fine-scale analysis of soil organic carbon composition under different temperature gradients and characterized the corresponding microbial growth and physiology across various paddy soils spanning 4000 km in China. Our results showed that warming altered the composition of organic matter, resulting in a reduction in carbohydrates of approximately 0.026% to 0.030% from humid subtropical regions to humid continental regions. These changes were attributed to a decrease in the proportion of cold-preferring bacteria, leading to significant soil carbon losses. Our findings suggest that intrinsic microbial temperature sensitivity plays a crucial role in determining the rate of soil organic carbon decomposition, providing insights into the temperature limitations faced by microbial activities and their impact on soil carbon-climate feedback.
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Affiliation(s)
- Sen Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Nanjing, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Jixian Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Han Hu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weigen Huang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yishen Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haowei Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanyun Kuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Jizhong Zhou
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Nanjing, China
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4
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Gao X, Zheng Z, Diao Z, Zhang Y, Wang Y, Ma L. The effects of litter input and increased precipitation on soil microbial communities in a temperate grassland. Front Microbiol 2024; 15:1347016. [PMID: 38650869 PMCID: PMC11033436 DOI: 10.3389/fmicb.2024.1347016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/15/2024] [Indexed: 04/25/2024] Open
Abstract
Global warming has contributed to shifts in precipitation patterns and increased plant productivity, resulting in a significant increase in litter input into the soils. The enhanced litter input, combined with higher levels of precipitation, may potentially affect soil microbial communities. This study aims to investigate the effects of litter input and increased precipitation on soil microbial biomass, community structure, and diversity in a temperate meadow steppe in northeastern China. Different levels of litter input (0%, +30%, +60%) and increased precipitation (0%, +15%, +30%) were applied over a three-year period (2015-2017). The results showed that litter input significantly increased the biomass of bacteria and fungi without altering their diversity, as well as the ratio of bacterial to fungal biomass. Increased precipitation did not have a notable effect on the biomass and diversity of bacteria and fungi, but it did increase the fungal-to-bacterial biomass ratio. However, when litter input and increased precipitation interacted, bacterial diversity significantly increased while the fungal-to-bacterial biomass ratio remained unchanged. These findings indicate that the projected increases in litter and precipitation would have a substantial impact on soil microbial communities. In energy-and water-limited temperate grasslands, the additional litter inputs and increased precipitation contribute to enhanced nutrient and water availability, which in turn promotes microbial growth and leads to shifts in community structure and diversity.
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Affiliation(s)
- Xiuli Gao
- Institute of Ecology, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Zhirong Zheng
- Institute of Ecology, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Zhaoyan Diao
- Institute of Ecology, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Yeming Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Yupei Wang
- International Economics and Trade, University of Technology, Beijing, China
| | - Linna Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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5
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Kimball S, Rath J, Coffey JE, Perea-Vega MR, Walsh M, Fiore NM, Ta PM, Schmidt KT, Goulden ML, Allison SD. Long-term drought promotes invasive species by reducing wildfire severity. Ecology 2024; 105:e4265. [PMID: 38380597 DOI: 10.1002/ecy.4265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/06/2023] [Accepted: 12/21/2023] [Indexed: 02/22/2024]
Abstract
Anthropogenic climate change has increased the frequency of drought, wildfire, and invasions of non-native species. Although high-severity fires linked to drought can inhibit recovery of native vegetation in forested ecosystems, it remains unclear how drought impacts the recovery of other plant communities following wildfire. We leveraged an existing rainfall manipulation experiment to test the hypothesis that reduced precipitation, fuel load, and fire severity convert plant community composition from native shrubs to invasive grasses in a Southern California coastal sage scrub system. We measured community composition before and after the 2020 Silverado wildfire in plots with three rainfall treatments. Drought reduced fuel load and vegetation cover, which reduced fire severity. Native shrubs had greater prefire cover in added water plots compared to reduced water plots. Native cover was lower and invasive cover was higher in postfire reduced water plots compared to postfire added and ambient water plots. Our results demonstrate the importance of fuel load on fire severity and plant community composition on an ecosystem scale. Management should focus on reducing fire frequency and removing invasive species to maintain the resilience of coastal sage scrub communities facing drought. In these communities, controlled burns are not recommended as they promote invasive plants.
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Affiliation(s)
- Sarah Kimball
- Center for Environmental Biology, University of California, Irvine, California, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Jessica Rath
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Julie E Coffey
- UCI-Nature, University of California, Irvine, California, USA
| | - Moises R Perea-Vega
- Center for Environmental Biology, University of California, Irvine, California, USA
| | - Matthew Walsh
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Nicole M Fiore
- Center for Environmental Biology, University of California, Irvine, California, USA
| | - Priscilla M Ta
- Center for Environmental Biology, University of California, Irvine, California, USA
| | - Katharina T Schmidt
- Center for Environmental Biology, University of California, Irvine, California, USA
| | - Michael L Goulden
- Department of Earth System Science, University of California, Irvine, California, USA
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, California, USA
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6
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Barbour KM, Martiny JBH. Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system. THE ISME JOURNAL 2024; 18:wrae043. [PMID: 38506671 PMCID: PMC11008689 DOI: 10.1093/ismejo/wrae043] [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: 12/22/2023] [Revised: 02/13/2024] [Accepted: 03/19/2024] [Indexed: 03/21/2024]
Abstract
Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter-topmost layer of surface soil-is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in Southern California ecosystems. By leveraging a number of methodological advantages of the system, we have worked to demonstrate how four processes-selection, dispersal, drift, and diversification-contribute to bacterial and fungal community assembly and ultimately impact community functioning. Although many dimensions remain to be investigated, our initial results demonstrate that both ecological and evolutionary processes occur simultaneously to influence microbial community assembly. We propose that the development of additional and experimentally tractable microbial systems will be enormously valuable to test the role of eco-evolutionary processes in natural settings and their implications in the face of rapid global change.
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Affiliation(s)
- Kristin M Barbour
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, United States
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, United States
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7
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Lei J, Su Y, Jian S, Guo X, Yuan M, Bates CT, Shi ZJ, Li J, Su Y, Ning D, Wu L, Zhou J, Yang Y. Warming effects on grassland soil microbial communities are amplified in cool months. THE ISME JOURNAL 2024; 18:wrae088. [PMID: 38747385 PMCID: PMC11170927 DOI: 10.1093/ismejo/wrae088] [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: 01/10/2024] [Revised: 03/25/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024]
Abstract
Global warming modulates soil respiration (RS) via microbial decomposition, which is seasonally dependent. Yet, the magnitude and direction of this modulation remain unclear, partly owing to the lack of knowledge on how microorganisms respond to seasonal changes. Here, we investigated the temporal dynamics of soil microbial communities over 12 consecutive months under experimental warming in a tallgrass prairie ecosystem. The interplay between warming and time altered (P < 0.05) the taxonomic and functional compositions of microbial communities. During the cool months (January to February and October to December), warming induced a soil microbiome with a higher genomic potential for carbon decomposition, community-level ribosomal RNA operon (rrn) copy numbers, and microbial metabolic quotients, suggesting that warming stimulated fast-growing microorganisms that enhanced carbon decomposition. Modeling analyses further showed that warming reduced the temperature sensitivity of microbial carbon use efficiency (CUE) by 28.7% when monthly average temperature was low, resulting in lower microbial CUE and higher heterotrophic respiration (Rh) potentials. Structural equation modeling showed that warming modulated both Rh and RS directly by altering soil temperature and indirectly by influencing microbial community traits, soil moisture, nitrate content, soil pH, and gross primary productivity. The modulation of Rh by warming was more pronounced in cooler months compared to warmer ones. Together, our findings reveal distinct warming-induced effects on microbial functional traits in cool months, challenging the norm of soil sampling only in the peak growing season, and advancing our mechanistic understanding of the seasonal pattern of RS and Rh sensitivity to warming.
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Affiliation(s)
- Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Yuanlong Su
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Siyang Jian
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94704, United States
| | - Colin T Bates
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Zhou Jason Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences and Environmental Microbiology & Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Yifan Su
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Daliang Ning
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Liyou Wu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, United States
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019, United States
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
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8
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Scales NC, Huynh KT, Weihe C, Martiny JBH. Desiccation induces varied responses within a soil bacterial genus. Environ Microbiol 2023; 25:3075-3086. [PMID: 37664956 DOI: 10.1111/1462-2920.16494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/02/2023] [Indexed: 09/05/2023]
Abstract
Desiccation impacts a suite of physiological processes in microbes by elevating levels of damaging reactive oxygen species and inducing DNA strand breaks. In response to desiccation-induced stress, microbes have evolved specialized mechanisms to help them survive. Here, we performed a 128-day lab desiccation experiment on nine strains from three clades of an abundant soil bacterium, Curtobacterium. We sequenced RNA from each strain at three time points to investigate their response. Curtobacterium was highly resistant to desiccation, outlasting both Escherichia coli and a famously DNA damage-resistant bacterium, Deinococcus radiodurans. However, within the genus, there were also 10-fold differences in survival rates among strains. Transcriptomic profiling revealed responses shared within the genus including up-regulation of genes involved in DNA damage repair, osmolyte production, and efflux pumps, but also up-regulation of pathways and genes unique to the three clades. For example, trehalose synthesis gene otsB, the chaperone groEL, and the oxygen scavenger katA were all found in either one or two clades but not the third. Here, we provide evidence of considerable variation in closely related strains, and further elucidation of the phylogenetic conservation of desiccation tolerance remains an important goal for microbial ecologists.
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Affiliation(s)
- N C Scales
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - K T Huynh
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - C Weihe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - J B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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9
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Feng GD, Li J, Yang S, Zhang J, Zhu H. Curtobacterium caseinilyticum sp. nov., Curtobacterium subtropicum sp. nov. and Curtobacterium citri sp. nov., isolated from citrus phyllosphere. Int J Syst Evol Microbiol 2023; 73. [PMID: 37938092 DOI: 10.1099/ijsem.0.006152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
Three novel Gram-stain-positive, aerobic and rod-shaped bacterial strains, designated RHCKG28T, RHCJP20T and RHCKG23T, were isolated from phyllosphere of healthy citrus leaves collected from Renhua County in Guangdong Province, PR China. 16S rRNA gene sequences comparison and phylogenetic analyses showed that they all belonged to the genus Curtobacterium, among which strain RHCKG28T showed the highest similarity to Curtobacterium herbarum NBRC 103064T (99.3 %), while strains RHCJP20T and RHCKG23T showed 99.2 and 99.0 % similarity to Curtobacterium citreum JCM 1345T, respectively. Phylogenomic analysis showed that the three novel strains were most closely related to C. citreum JCM 1345T and Curtobacterium albidum JCM 1344T. The novel strains could be distinguished from their closely related type strains in terms of enzyme activities, substrate assimilation and fatty acid profiles. In addition, the average nucleotide identity and digital DNA-DNA hybridization values between the novel strains and closely related type strains were 84.4‒89.5 % and 24.5‒34.1 %, respectively, which were below the threshold values for species delimitation. They all took anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as the major fatty acids, menaquinone 9 (MK-9) as the sole predominant respiratory quinone, and ornithine as the principal cell-wall diamino acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and several unidentified glycolipids. The phenotypic, genotypic and chemotaxonomic data supported that they represent three distinct novel species of the genus Curtobacterium, for which the names Curtobacterium caseinilyticum sp. nov., Curtobacterium subtropicum sp. nov. and Curtobacterium citri sp. nov. are proposed, with RHCKG28T (=GDMCC 1.2667T=JCM 34828T), RHCJP20T (=GDMCC 1.2668T=JCM 34829T) and RHCKG23T (=GDMCC 1.2669T=JCM 34830T) as the type strains, respectively.
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Affiliation(s)
- Guang-Da Feng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Jiali Li
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, PR China
| | - Songzhen Yang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Jun Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
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10
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Benincà E, Pinto S, Cazelles B, Fuentes S, Shetty S, Bogaards JA. Wavelet clustering analysis as a tool for characterizing community structure in the human microbiome. Sci Rep 2023; 13:8042. [PMID: 37198426 PMCID: PMC10192422 DOI: 10.1038/s41598-023-34713-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/05/2023] [Indexed: 05/19/2023] Open
Abstract
Human microbiome research is helped by the characterization of microbial networks, as these may reveal key microbes that can be targeted for beneficial health effects. Prevailing methods of microbial network characterization are based on measures of association, often applied to limited sampling points in time. Here, we demonstrate the potential of wavelet clustering, a technique that clusters time series based on similarities in their spectral characteristics. We illustrate this technique with synthetic time series and apply wavelet clustering to densely sampled human gut microbiome time series. We compare our results with hierarchical clustering based on temporal correlations in abundance, within and across individuals, and show that the cluster trees obtained by using either method are significantly different in terms of elements clustered together, branching structure and total branch length. By capitalizing on the dynamic nature of the human microbiome, wavelet clustering reveals community structures that remain obscured in correlation-based methods.
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Affiliation(s)
- Elisa Benincà
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
| | - Susanne Pinto
- Biomedical Data Sciences, Leiden UMC, Leiden, The Netherlands
| | - Bernard Cazelles
- CNRS UMR-8197, IBENS, Ecole Normale Supérieure, Paris, France
- Sorbonne Université, UMMISCO, Paris, France
| | - Susana Fuentes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sudarshan Shetty
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Medical Microbiology and Infection Prevention, UMC Groningen, Groningen, The Netherlands
| | - Johannes A Bogaards
- Department of Epidemiology & Data Science, Amsterdam UMC location VUMC, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Amsterdam, The Netherlands
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11
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Allison SD. Microbial drought resistance may destabilize soil carbon. Trends Microbiol 2023:S0966-842X(23)00078-1. [PMID: 37059647 DOI: 10.1016/j.tim.2023.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/09/2023] [Accepted: 03/02/2023] [Indexed: 04/16/2023]
Abstract
Droughts are becoming more frequent and intense with climate change. As plants and microbes respond to drought, there may be consequences for the vast stocks of organic carbon stored in soils. If microbes sustain their activity under drought, soils could lose carbon, especially if inputs from plants decline. Empirical and theoretical studies reveal multiple mechanisms of microbial drought resistance, including tolerance and avoidance. Physiological responses allow microbes to acclimate to drought within minutes to days. Along with dispersal, shifts in community composition could allow microbiomes to maintain functioning despite drought. Microbes might also adapt to drier conditions through evolutionary processes. Together, these mechanisms could result in soil carbon losses larger than currently anticipated under climate change.
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Affiliation(s)
- Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA; Department of Earth System Science, University of California, Irvine, CA, USA.
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12
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Clay NA, Herrmann MC, Evans-White MA, Entrekin SA, West C. Sodium as a subsidy in the spring: evidence for a phenology of sodium limitation. Oecologia 2023; 201:783-795. [PMID: 36853383 PMCID: PMC10038971 DOI: 10.1007/s00442-023-05336-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/10/2023] [Indexed: 03/01/2023]
Abstract
Understanding the factors that mediate carbon (C) cycling is increasingly important as anthropogenic activities and climate change alter ecosystems. Decomposition rates mediate C cycling and are in part regulated by sodium (Na) where Na is limiting up to some threshold after which Na becomes stressful and reduces decomposition rates (i.e., the Sodium Subsidy-Stress hypothesis). An overlooked pathway by which decomposers encounter increased salts like NaCl is through plants, which often take up Na in proportion to soil concentrations. Here we tested the hypothesis that Na addition through litter (detritus) and water and their interaction would impact detrital processing and leachate chemistry. Laboratory riparian soil mesocosms received either artificial litter (100% cellulose sponges) soaked in 0.05% NaCl (NaClL) or just H2O (H2OL: control) and half of each litter treatment received weekly additions of 150 ml of either 0.05% NaCl water (NaClW) or just H2O (H2OW: control). After 8 weeks decomposition was higher in NaCl addition treatments (both NaClL and NaClW and their combo) than controls (H2OL + H2OW) but reflected a unimodal relationship where the saltiest treatment (NaClL + NaClW) was only marginally higher than controls indicating a subsidy-stress response. Previous studies in this system found that Na addition in either water or litter decreased decomposition. However, differences may reflect a phenology of Na demand where Na-limitation increases in the spring (this study). These results indicate that our understanding of how Na impacts detrital processes, C cycling, and aquatic-terrestrial linkages necessitates incorporation of temporal dynamics.
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Affiliation(s)
- Natalie A Clay
- School of Biological Sciences, Louisiana Tech University, 1 Adams Blvd., Ruston, LA, 71272, USA.
| | - Maggie C Herrmann
- School of Biological Sciences, Louisiana Tech University, 1 Adams Blvd., Ruston, LA, 71272, USA
| | - Michelle A Evans-White
- Department of Biological Sciences, University of Arkansas, 525 Old Main, Fayetteville, AR, 72701, USA
| | - Sally A Entrekin
- Department of Entomology, Virginia Tech, 170 Drillfield Drive, Blacksburg, VA, 24061, USA
| | - Colton West
- School of Biological Sciences, Louisiana Tech University, 1 Adams Blvd., Ruston, LA, 71272, USA
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13
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Larson CE, Engelken P, McCullough DG, Eric Benbow M. Emerald ash borer invasion of riparian forests alters organic matter and bacterial subsidies to south Michigan headwater streams. CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES. JOURNAL CANADIEN DES SCIENCES HALIEUTIQUES ET AQUATIQUES 2023; 80:298-312. [PMID: 37942173 PMCID: PMC10631550 DOI: 10.1139/cjfas-2022-0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Emerald ash borer (EAB) has killed millions of ash trees in the United States and Canada, yet impacts on terrestrial-aquatic linkages are largely unknown. Ash tree death along streams creates canopy gaps, increasing light to riparian plants and potentially affecting organic matter subsidies. Six EAB-related canopy gaps along streams across a gradient of timing of EAB invasion in Michigan were characterized for coarse woody material (CWM), terrestrial and aquatic leaf litter and their associated bacterial communities, and macroinvertebrates upstream, downstream, and at the center of the gap. Stream sites downstream of EAB-related canopy gaps had significantly lower dissolved oxygen and macroinvertebrate diversity than sites upstream and at the gaps. Yet there was no difference in CWM or aquatic leaf litter, likely due to downstream movement of organic matter from upstream riparian sources. Low abundance bacterial amplicon sequence variants unique to gap or forest were detected in leaves and leaf litter, suggesting that EAB-related canopy gaps altered leaf-associated bacterial communities. Overall, EAB invasion indirectly impacted some variables, while organic matter dynamics were resistant to change.
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Affiliation(s)
- Courtney E. Larson
- Department of Entomology, Michigan State University, Natural Science Building. 288, Farm Lane Room 243, East Lansing, MI, 48824, USA
- Ecology, Evolution and Behavior Program, Michigan State University, 103 Giltner Hall, 293 Farm Lane, Room 103, East Lansing, MI 48824, USA
| | - Patrick Engelken
- Department of Entomology, Michigan State University, Natural Science Building. 288, Farm Lane Room 243, East Lansing, MI, 48824, USA
| | - Deborah G. McCullough
- Department of Entomology, Michigan State University, Natural Science Building. 288, Farm Lane Room 243, East Lansing, MI, 48824, USA
- Department of Forestry, Michigan State University, Natural Resources Building, 480 Wilson Road, Room 126, East Lansing, MI 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI 48824, USA
| | - M. Eric Benbow
- Department of Entomology, Michigan State University, Natural Science Building. 288, Farm Lane Room 243, East Lansing, MI, 48824, USA
- Ecology, Evolution and Behavior Program, Michigan State University, 103 Giltner Hall, 293 Farm Lane, Room 103, East Lansing, MI 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI 48824, USA
- Department of Osteopathic Medical Specialties, Michigan State University, 965 Wilson Road, East Lansing, MI 48824, USA
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14
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Khanal M, Bhatta BP, Timilsina S, Ghimire S, Cochran K, Malla S. Curtobacterium allii sp. nov., the actinobacterial pathogen causing onion bulb rot. Antonie Van Leeuwenhoek 2023; 116:83-96. [PMID: 36100777 DOI: 10.1007/s10482-022-01775-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/06/2022] [Indexed: 02/01/2023]
Abstract
A Gram-stain-positive, aerobic, and non-spore-forming bacterial strain, 20TX0166T, was isolated from a diseased onion bulb in Texas, USA. Upon testing its pathogenicity on onion bulb, it produced pathogenic response which makes it first species of pathogen belonging to the phylum actinobacteria detected in onion. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the strain belonged to the genus Curtobacterium and was most similar to Curtobacterium flaccumfaciens LMG 3645T (100%), C. pusillum DSM 20527T (99.5%), and C. oceanosedimentum ATCC 31317T (99.5%). The estimated genome size of the novel species was 4.0 Mbp with a G + C content of 70.8%. The orthologous ANI (orthoANIu), ANI based on blast (ANIb), and dDDH values between the novel strain and the closest relative, C. flaccumfaciens LMG 3645T, were 95.7%, 95.4%, and 63.3%, respectively. These values were below the recommended species cut-off threshold of 96% (ANI) and 70% (dDDH), suggesting the strain may be a novel species. Physiologic and phenotypic characters of this novel strain were also unique when compared with the closely related species. The major cellular fatty acids of this strain were anteiso-C15:0 and anteiso-C17:0. Using a polyphasic approach based on phenotypic and genotypic analyses, strain 20TX0166T represents a novel species of the genus Curtobacterium, and the name Curtobacterium allii sp. nov. is proposed. The type strain is 20TX0166T (= LMG 32517T = CIP112023T = NCIMB 15427T).
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Affiliation(s)
- Manzeal Khanal
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA.,Texas A&M AgriLife Research and Extension Centre, Uvalde, TX, 78801, USA
| | - Bed Prakash Bhatta
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA.,Texas A&M AgriLife Research and Extension Centre, Uvalde, TX, 78801, USA
| | - Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA.,Charles River Laboratories, Newark, DE, USA
| | - Sudeep Ghimire
- Department of Pathology, University of Iowa, Iowa City, IA, 54442, USA
| | - Kimberly Cochran
- Texas A&M AgriLife Research and Extension Centre, Uvalde, TX, 78801, USA.,Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Subas Malla
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA. .,Texas A&M AgriLife Research and Extension Centre, Uvalde, TX, 78801, USA.
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15
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Abs E, Chase AB, Allison SD. How do soil microbes shape ecosystem biogeochemistry in the context of global change? Environ Microbiol 2022; 25:780-785. [PMID: 36579433 DOI: 10.1111/1462-2920.16331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 12/30/2022]
Affiliation(s)
- Elsa Abs
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, Dallas, Texas, USA
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA.,Department of Earth System Science, University of California, Irvine, California, USA
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16
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Walters KE, Capocchi JK, Albright MBN, Hao Z, Brodie EL, Martiny JBH. Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning. THE ISME JOURNAL 2022; 16:2295-2304. [PMID: 35778440 PMCID: PMC9477824 DOI: 10.1038/s41396-022-01269-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 12/21/2022]
Abstract
Recent evidence suggests that, similar to larger organisms, dispersal is a key driver of microbiome assembly; however, our understanding of the rates and taxonomic composition of microbial dispersal in natural environments is limited. Here, we characterized the rate and composition of bacteria dispersing into surface soil via three dispersal routes (from the air above the vegetation, from nearby vegetation and leaf litter near the soil surface, and from the bulk soil and litter below the top layer). We then quantified the impact of those routes on microbial community composition and functioning in the topmost litter layer. The bacterial dispersal rate onto the surface layer was low (7900 cells/cm2/day) relative to the abundance of the resident community. While bacteria dispersed through all three routes at the same rate, only dispersal from above and near the soil surface impacted microbiome composition, suggesting that the composition, not rate, of dispersal influenced community assembly. Dispersal also impacted microbiome functioning. When exposed to dispersal, leaf litter decomposed faster than when dispersal was excluded, although neither decomposition rate nor litter chemistry differed by route. Overall, we conclude that the dispersal routes transport distinct bacterial communities that differentially influence the composition of the surface soil microbiome.
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Affiliation(s)
- Kendra E Walters
- Department of Ecology and Evolutionary Biology, University of California - Irvine, Irvine, CA, USA.
| | - Joia K Capocchi
- Department of Ecology and Evolutionary Biology, University of California - Irvine, Irvine, CA, USA
| | | | - Zhao Hao
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California - Irvine, Irvine, CA, USA
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17
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Guo X, Yuan M, Lei J, Shi Z, Zhou X, Li J, Deng Y, Yang Y, Wu L, Luo Y, Tiedje JM, Zhou J. Climate warming restructures seasonal dynamics of grassland soil microbial communities. MLIFE 2022; 1:245-256. [PMID: 38818216 PMCID: PMC10989843 DOI: 10.1002/mlf2.12035] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/07/2022] [Accepted: 07/09/2022] [Indexed: 06/01/2024]
Abstract
Soil microbial community's responses to climate warming alter the global carbon cycle. In temperate ecosystems, soil microbial communities function along seasonal cycles. However, little is known about how the responses of soil microbial communities to warming vary when the season changes. In this study, we investigated the seasonal dynamics of soil bacterial community under experimental warming in a temperate tall-grass prairie ecosystem. Our results showed that warming significantly (p = 0.001) shifted community structure, such that the differences of microbial communities between warming and control plots increased nonlinearly (R 2 = 0.578, p = 0.021) from spring to winter. Also, warming significantly (p < 0.050) increased microbial network complexity and robustness, especially during the colder seasons, despite large variations in network size and complexity in different seasons. In addition, the relative importance of stochastic processes in shaping the microbial community decreased by warming in fall and winter but not in spring and summer. Our study indicates that climate warming restructures the seasonal dynamics of soil microbial community in a temperate ecosystem. Such seasonality of microbial responses to warming may enlarge over time and could have significant impacts on the terrestrial carbon cycle.
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Affiliation(s)
- Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
- Institute for Environmental Genomics and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - Zhou Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
- Gladstone Institutes and Chan‐Zuckerberg BiohubSan FranciscoCaliforniaUSA
| | - Xishu Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
- School of Minerals Processing and BioengineeringCentral South UniversityChangshaChina
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences and Environmental Microbiology, & Key Laboratory of Sichuan Province, Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - Liyou Wu
- Institute for Environmental Genomics and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Yiqi Luo
- Department of Biological Sciences, Center for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
| | - James M. Tiedje
- Center for Microbial EcologyMichigan State UniversityEast LansingMichiganUSA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA
- School of Civil Engineering and Environmental SciencesUniversity of OklahomaNormanOklahomaUSA
- Earth and Environmental SciencesLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
- School of Computer SciencesUniversity of OklahomaNormanOklahomaUSA
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18
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Alster CJ, Allison SD, Treseder KK. Trait relationships of fungal decomposers in response to drought using a dual field and laboratory approach. Ecosphere 2022. [DOI: 10.1002/ecs2.4063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Charlotte J. Alster
- Ecology and Evolutionary Biology University of California Irvine Irvine California USA
| | - Steven D. Allison
- Ecology and Evolutionary Biology University of California Irvine Irvine California USA
- Department of Earth System Science University of California Irvine Irvine California USA
| | - Kathleen K. Treseder
- Ecology and Evolutionary Biology University of California Irvine Irvine California USA
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19
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You F, Lu P, Huang L. Characteristics of prokaryotic and fungal communities emerged in eco-engineered waste rock - Eucalyptus open woodlands at Ranger uranium mine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151571. [PMID: 34767894 DOI: 10.1016/j.scitotenv.2021.151571] [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: 08/18/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
Diverse prokaryotic and fungal communities in soil and litters are the structural basis for driving tree litter decomposition and inherent nutrient cycling in infertile Eucalyptus open woodlands. The present investigation characterized the composition and co-occurrence network of prokaryotic and fungal communities in litter and surface soil layers in 9-year old revegetated trial landforms at Ranger uranium mine, Northern Territory, Australia. The revegetated landforms consisted of soil-subsystems engineered from waste rocks and plant-subsystems of young, novel and native Eucalyptus open woodlands. The analysis of litters and surface soil layer revealed highly diverse microbial communities in the young Eucalyptus open woodland systems, which were composed of an average 1155 prokaryotic and 236 fungal OTUs. In the microbial communities, abundant bacterial communities were affiliated to Actinobacteria (30.2%), Proteobacteria (25.3%) and Chloroflexi (16.9%); and fungal communities were highly dominated by Ascomycota (63.4%) and Basidiomycota (23.6%). These OTUs were highly connected, forming microbial modules with >50% of predicted genes associated with metabolism of organics in the open woodland. Soil microbial communities present in the wet season contained a relatively high abundance of ammonium oxidizing archaea, plant associated bacteria, and fungal groups adapted to higher N availability, particularly those from the laterite + waste rock site. The elevated microbial activities in the litters and surface soil of lateritic soil + waste rock landform were attributed to the improved water and nutrient availability by increased fine fraction of laterites. Our study provides evidence that the features of prokaryotic and fungal communities in this eco-engineered and young waste rock - open Eucalyptus woodland systems are consistent with characteristics of microbial communities of native Eucalyptus woodlands to drive the decomposition of low N tree litters.
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Affiliation(s)
- Fang You
- Sustainable Minerals Institute, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Ping Lu
- Sustainable Minerals Institute, The University of Queensland, Brisbane, Qld 4072, Australia; Energy Resources of Australia, Darwin, NT 0800, Australia
| | - Longbin Huang
- Sustainable Minerals Institute, The University of Queensland, Brisbane, Qld 4072, Australia.
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20
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Differential Response of Bacterial Microdiversity to Simulated Global Change. Appl Environ Microbiol 2022; 88:e0242921. [PMID: 35108096 PMCID: PMC8939344 DOI: 10.1128/aem.02429-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Global change experiments often observe shifts in bacterial community composition based on 16S rRNA gene sequences. However, this genetic region can mask a large amount of genetic and phenotypic variation among bacterial strains sharing even identical 16S regions. As such, it remains largely unknown whether variation at the sub-16S level, sometimes termed microdiversity, responds to environmental perturbations and whether such changes are relevant to ecosystem processes. Here, we investigated microdiversity within Curtobacterium, the dominant bacterium found in the leaf litter layer of soil, to simulated drought and nitrogen addition in a field experiment. We first developed and validated Curtobacterium-specific primers of the groEL gene to assess microdiversity within this lineage. We then tracked the response of this microdiversity to simulated global change in two adjacent plant communities, grassland and coastal sage scrub (CSS). Curtobacterium microdiversity responded to drought but not nitrogen addition, indicating variation within the genus of drought tolerance but not nitrogen response. Further, the response of microdiversity to drought depended on the ecosystem, suggesting that litter substrate selects for a distinct composition of microdiversity that is constrained in its response, perhaps related to tradeoffs in resource acquisition traits. Supporting this interpretation, a metagenomic analysis revealed that the composition of Curtobacterium-encoded CAZymes varied distinctly across the two ecosystems. Identifying the degree to which relevant traits are phylogenetically conserved may help to predict when the aggregated response of a 16S-defined taxon masks differential responses of finer-scale bacterial diversity to global change. Importance Microbial communities play an integral role in global biogeochemical cycling, but our understanding of how global change will affect microbial community structure and functioning remains limited. Microbiome analyses typically aggregate large amounts of genetic diversity which may obscure finer variation in traits. This study found that fine-scale diversity (or microdiversity) within the bacterial genus, Curtobacterium, was affected by simulated global changes. However, the degree to which this was true depended on the type of global change as the composition of Curtobacterium microdiversity was affected by drought, but not by nitrogen addition. Further, these changes were associated with variation in carbon degradation traits. Future work might improve predictions of microbial community responses to global change by considering microdiversity.
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21
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Alster CJ, Allison SD, Johnson NG, Glassman SI, Treseder KK. Phenotypic plasticity of fungal traits in response to moisture and temperature. ISME COMMUNICATIONS 2021; 1:43. [PMID: 36740602 PMCID: PMC9723763 DOI: 10.1038/s43705-021-00045-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/13/2021] [Accepted: 07/23/2021] [Indexed: 02/07/2023]
Abstract
Phenotypic plasticity of traits is commonly measured in plants to improve understanding of organismal and ecosystem responses to climate change but is far less studied for microbes. Specifically, decomposer fungi are thought to display high levels of phenotypic plasticity and their functions have important implications for ecosystem dynamics. Assessing the phenotypic plasticity of fungal traits may therefore be important for predicting fungal community response to climate change. Here, we assess the phenotypic plasticity of 15 fungal isolates (12 species) from a Southern California grassland. Fungi were incubated on litter at five moisture levels (ranging from 4-50% water holding capacity) and at five temperatures (ranging from 4-36 °C). After incubation, fungal biomass and activities of four extracellular enzymes (cellobiohydrolase (CBH), β-glucosidase (BG), β-xylosidase (BX), and N-acetyl-β-D-glucosaminidase (NAG)) were measured. We used response surface methodology to determine how fungal phenotypic plasticity differs across the moisture-temperature gradient. We hypothesized that fungal biomass and extracellular enzyme activities would vary with moisture and temperature and that the shape of the response surface would vary between fungal isolates. We further hypothesized that more closely related fungi would show more similar response surfaces across the moisture-temperature gradient. In support of our hypotheses, we found that plasticity differed between fungi along the temperature gradient for fungal biomass and for all the extracellular enzyme activities. Plasticity also differed between fungi along the moisture gradient for BG activity. These differences appear to be caused by variation mainly at the moisture and temperature extremes. We also found that more closely related fungi had more similar extracellular enzymes activities at the highest temperature. Altogether, this evidence suggests that with global warming, fungal biodiversity may become increasingly important as functional traits tend to diverge along phylogenetic lines at higher temperatures.
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Affiliation(s)
- Charlotte J Alster
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA.
- School of Science, University of Waikato, Hamilton, New Zealand.
| | - Steven D Allison
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, Irvine, CA, USA
| | - Nels G Johnson
- USDA Forest Service, Pacific Southwest Research Station, Albany, CA, USA
| | - Sydney I Glassman
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Kathleen K Treseder
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
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22
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Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient. Proc Natl Acad Sci U S A 2021; 118:2101254118. [PMID: 33906949 PMCID: PMC8106337 DOI: 10.1073/pnas.2101254118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Increasing evidence suggests that evolutionary processes frequently shape ecological patterns; however, most microbiome studies thus far have focused on only the ecological responses of these communities. By using parallel field experiments and focusing in on a model soil bacterium, we showed that bacterial “species” are differentially adapted to local climates, leading to changes in their composition. Furthermore, we detected strain-level evolution, providing direct evidence that both ecological and evolutionary processes operate on annual timescales. The consideration of eco-evolutionary dynamics may therefore be important to understand the response of soil microbiomes to future environmental change. Microbial community responses to environmental change are largely associated with ecological processes; however, the potential for microbes to rapidly evolve and adapt remains relatively unexplored in natural environments. To assess how ecological and evolutionary processes simultaneously alter the genetic diversity of a microbiome, we conducted two concurrent experiments in the leaf litter layer of soil over 18 mo across a climate gradient in Southern California. In the first experiment, we reciprocally transplanted microbial communities from five sites to test whether ecological shifts in ecotypes of the abundant bacterium, Curtobacterium, corresponded to past adaptive differentiation. In the transplanted communities, ecotypes converged toward that of the native communities growing on a common litter substrate. Moreover, these shifts were correlated with community-weighted mean trait values of the Curtobacterium ecotypes, indicating that some of the trait variation among ecotypes could be explained by local adaptation to climate conditions. In the second experiment, we transplanted an isogenic Curtobacterium strain and tracked genomic mutations associated with the sites across the same climate gradient. Using a combination of genomic and metagenomic approaches, we identified a variety of nonrandom, parallel mutations associated with transplantation, including mutations in genes related to nutrient acquisition, stress response, and exopolysaccharide production. Together, the field experiments demonstrate how both demographic shifts of previously adapted ecotypes and contemporary evolution can alter the diversity of a soil microbiome on the same timescale.
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23
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Alster CJ, Allison SD, Glassman SI, Martiny AC, Treseder KK. Exploring Trait Trade-Offs for Fungal Decomposers in a Southern California Grassland. Front Microbiol 2021; 12:655987. [PMID: 33995318 PMCID: PMC8118720 DOI: 10.3389/fmicb.2021.655987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 11/14/2022] Open
Abstract
Fungi are important decomposers in terrestrial ecosystems, so their responses to climate change might influence carbon (C) and nitrogen (N) dynamics. We investigated whether growth and activity of fungi under drought conditions were structured by trade-offs among traits in 15 fungal isolates from a Mediterranean Southern California grassland. We inoculated fungi onto sterilized litter that was incubated at three moisture levels (4, 27, and 50% water holding capacity, WHC). For each isolate, we characterized traits that described three potential lifestyles within the newly proposed “YAS” framework: growth yield, resource acquisition, and stress tolerance. Specifically, we measured fungal hyphal length per unit litter decomposition for growth yield; the potential activities of the extracellular enzymes cellobiohydrolase (CBH), β-glucosidase (BG), β-xylosidase (BX), and N-acetyl-β-D-glucosaminidase (NAG) for resource acquisition; and ability to grow in drought vs. higher moisture levels for drought stress tolerance. Although, we had hypothesized that evolutionary and physiological trade-offs would elicit negative relationships among traits, we found no supporting evidence for this hypothesis. Across isolates, growth yield, drought stress tolerance, and extracellular enzyme activities were not significantly related to each other. Thus, it is possible that drought-induced shifts in fungal community composition may not necessarily lead to changes in fungal biomass or decomposer ability in this arid grassland.
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Affiliation(s)
- Charlotte J Alster
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
| | - Steven D Allison
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.,Department of Earth System Science, University of California Irvine, Irvine, CA, United States
| | - Sydney I Glassman
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States
| | - Adam C Martiny
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States.,Department of Earth System Science, University of California Irvine, Irvine, CA, United States
| | - Kathleen K Treseder
- Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
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24
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Logan JR, Jacobson KM, Jacobson PJ, Evans SE. Fungal Communities on Standing Litter Are Structured by Moisture Type and Constrain Decomposition in a Hyper-Arid Grassland. Front Microbiol 2021; 12:596517. [PMID: 33716999 PMCID: PMC7943874 DOI: 10.3389/fmicb.2021.596517] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/03/2021] [Indexed: 12/26/2022] Open
Abstract
Non-rainfall moisture (fog, dew, and water vapor; NRM) is an important driver of plant litter decomposition in grasslands, where it can contribute significantly to terrestrial carbon cycling. However, we still do not know whether microbial decomposers respond differently to NRM and rain, nor whether this response affects litter decomposition rates. To determine how local moisture regimes influence decomposer communities and their function, we examined fungal communities on standing grass litter at an NRM-dominated site and a rain-dominated site 75 km apart in the hyper-arid Namib Desert using a reciprocal transplant design. Dominant taxa at both sites consisted of both extremophilic and cosmopolitan species. Fungal communities differed between the two moisture regimes with environment having a considerably stronger effect on community composition than did stage of decomposition. Community composition was influenced by the availability of air-derived spores at each site and by specialization of fungi to their home environment; specifically, fungi from the cooler, moister NRM Site performed worse (measured as fungal biomass and litter mass loss) when moved to the warmer, drier rain-dominated site while Rain Site fungi performed equally well in both environments. Our results contribute to growing literature demonstrating that as climate change alters the frequency, magnitude and type of moisture events in arid ecosystems, litter decomposition rates may be altered and constrained by the composition of existing decomposer communities.
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Affiliation(s)
- J Robert Logan
- W.K. Kellogg Biological Station, Hickory Corners, MI, United States.,Department of Integrative Biology, Michigan State University, East Lansing, MI, United States.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
| | | | - Peter J Jacobson
- Department of Biology, Grinnell College, Grinnell, IA, United States
| | - Sarah E Evans
- W.K. Kellogg Biological Station, Hickory Corners, MI, United States.,Department of Integrative Biology, Michigan State University, East Lansing, MI, United States.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
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25
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Albright MBN, Johansen R, Thompson J, Lopez D, Gallegos-Graves LV, Kroeger ME, Runde A, Mueller RC, Washburne A, Munsky B, Yoshida T, Dunbar J. Soil Bacterial and Fungal Richness Forecast Patterns of Early Pine Litter Decomposition. Front Microbiol 2020; 11:542220. [PMID: 33240225 PMCID: PMC7677502 DOI: 10.3389/fmicb.2020.542220] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/13/2020] [Indexed: 12/22/2022] Open
Abstract
Discovering widespread microbial processes that drive unexpected variation in carbon cycling may improve modeling and management of soil carbon (Prescott, 2010; Wieder et al., 2015a, 2018). A first step is to identify community features linked to carbon cycle variation. We addressed this challenge using an epidemiological approach with 206 soil communities decomposing Ponderosa pine litter in 618 microcosms. Carbon flow from litter decomposition was measured over a 6-week incubation. Cumulative CO2 from microbial respiration varied two-fold among microcosms and dissolved organic carbon (DOC) from litter decomposition varied five-fold, demonstrating large functional variation despite constant environmental conditions where strong selection is expected. To investigate microbial features driving DOC concentration, two microbial community cohorts were delineated as "high" and "low" DOC. For each cohort, communities from the original soils and from the final microcosm communities after the 6-week incubation with litter were taxonomically profiled. A logistic model including total biomass, fungal richness, and bacterial richness measured in the original soils or in the final microcosm communities predicted the DOC cohort with 72 (P < 0.05) and 80 (P < 0.001) percent accuracy, respectively. The strongest predictors of the DOC cohort were biomass and either fungal richness (in the original soils) or bacterial richness (in the final microcosm communities). Successful forecasting of functional patterns after lengthy community succession in a new environment reveals strong historical contingencies. Forecasting future community function is a key advance beyond correlation of functional variance with end-state community features. The importance of taxon richness-the same feature linked to carbon fate in gut microbiome studies-underscores the need for increased understanding of biotic mechanisms that can shape richness in microbial communities independent of physicochemical conditions.
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Affiliation(s)
| | - Renee Johansen
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Jaron Thompson
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
| | - Deanna Lopez
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | | | - Marie E. Kroeger
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Andreas Runde
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Rebecca C. Mueller
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Alex Washburne
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Brian Munsky
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States
| | - Thomas Yoshida
- Chemical Diagnostics and Engineering, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - John Dunbar
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
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26
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Albright MBN, Sevanto S, Gallegos-Graves LV, Dunbar J. Biotic Interactions Are More Important than Propagule Pressure in Microbial Community Invasions. mBio 2020; 11:e02089-20. [PMID: 33109758 PMCID: PMC7593967 DOI: 10.1128/mbio.02089-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/07/2020] [Indexed: 01/08/2023] Open
Abstract
Microbial probiotics are intended to improve functions in diverse ecosystems, yet probiotics often fail to establish in a preexisting microbiome. This is a species invasion problem. The relative importance of the two major factors controlling establishment in this context-propagule pressure (inoculation dose and frequency) and biotic interactions (composition of introduced and resident communities)-is unknown. We tested the effect of these factors in driving microbial composition and functioning following 12 microbial community invasions (e.g., introductions of many microbial invaders) in microcosms. Ecosystem functioning over a 30-day postinvasion period was assessed by measuring activity (respiration) and environment modification (dissolved organic carbon abundance). To test the dependence on environmental context, experiments were performed in two resource environments. In both environments, biotic interactions were more important than propagule pressure in driving microbial composition and community function, but the magnitude of effect varied by environment. Successful invaders comprised approximately 8% of the total number of operational taxonomic units (OTUs). Bacteria were better invaders than fungi, with average relative abundances of 7.4% ± 6.8% and 1.5% ± 1.4% of OTUs, respectively. Common bacterial invaders were associated with stress response traits. The most resilient bacterial and fungal families, in other words, those least impacted by invasions, were linked to antimicrobial resistance or production traits. Illuminating the principles that determine community composition and functioning following microbial invasions is key to efficient community engineering.IMPORTANCE With increasing frequency, humans are introducing new microbes into preexisting microbiomes to alter functioning. Example applications include modification of microflora in human guts for better health and those of soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved with a better understanding of microbial invasions. We conducted a microbial community invasion experiment to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi).
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Affiliation(s)
| | - Sanna Sevanto
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | | | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico
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27
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Fahey C, Koyama A, Antunes PM, Dunfield K, Flory SL. Plant communities mediate the interactive effects of invasion and drought on soil microbial communities. THE ISME JOURNAL 2020; 14:1396-1409. [PMID: 32076127 PMCID: PMC7242364 DOI: 10.1038/s41396-020-0614-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 01/15/2020] [Accepted: 02/07/2020] [Indexed: 01/05/2023]
Abstract
Soil microbiomes could play a major role in ecosystem responses to escalating anthropogenic global change. However, we currently have a poor understanding of how soil microbes will respond to interacting global change factors and if responses will be mediated by changes in plant community structure. We used a field experiment to assess changes in soil fungal and bacterial communities in response to plant invasion, experimental drought, and their combination. In addition, we evaluated the relative importance of direct versus indirect pathways of invasion and drought through changes in associated plant communities with structural equation models. We found that fungal communities were interactively structured by invasion and drought, where fungal richness was lowest with invasion under ambient conditions but highest with invasion under drought conditions. Bacterial richness was lower under drought but unaffected by invasion. Changes in the plant community, including lower plant richness and higher root biomass, moderated the direct effects of invasion on microbial richness. Fungal and bacterial functional groups, including pathogens, mutualists, and nitrogen metabolizers, were also influenced by plant community changes. In sum, plant communities mediated the effects of interacting global change drivers on soil microbial community structure, with significant potential consequences for community dynamics and ecosystem functions.
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Affiliation(s)
- Catherine Fahey
- School of Natural Resources and Environment, University of Florida, Gainesville, FL, USA.
| | - Akihiro Koyama
- Department of Forestry, Michigan State University, East Lansing, MI, USA
| | - Pedro M Antunes
- Biology Department, Algoma University, Sault Ste. Marie, Ontario, Canada
| | - Kari Dunfield
- School of Environmental Science, University of Guelph, Guelph, ON, Canada
| | - S Luke Flory
- Agronomy Department, University of Florida, Gainesville, FL, USA
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28
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Shi Y, Zhang K, Li Q, Liu X, He JS, Chu H. Interannual climate variability and altered precipitation influence the soil microbial community structure in a Tibetan Plateau grassland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 714:136794. [PMID: 31991278 DOI: 10.1016/j.scitotenv.2020.136794] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Climate change could influence aboveground and belowground plant community diversity and structure profoundly. However, our understanding of the responses of microbial communities to changes in both temperature and precipitation remains poor. Here, using 16S rDNA and ITS high throughput sequencing, we investigated the responses of soil bacterial and fungal community structure to both temperature and precipitation changes, and how such changes could influence interannual variability within soil microbial communities in a grassland in the Tibetan Plateau. The altered precipitation treatments had significant effects on soil bacterial and fungal community structure (F = 2.11, P = 0,001; F = 2.26. P = 0.001, respectively), while year had a more significant effect on soil bacterial and fungal community structure (F = 3.36, P = 0.001; F = 2.67, P = 0.001, respectively). The results showed that the interannual fluctuations in mean annual precipitation and mean annual temperature were significantly correlated with the interannual variations in soil bacterial and fungal community structures. In addition, the robustness of co-occurrence relationships among microbes could be strongly influenced by the altered precipitation and year. Overall, our results indicated that the effect of interannual climate variability on the soil microbial community was greater than the effect of a 1.6 °C increase in temperature. Our findings suggest an interactive effect of rapid interannual variability and slow climate change on the belowground soil microbial community structure.
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Affiliation(s)
- Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Kaoping Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Qian Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jin-Sheng He
- Department of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
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29
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Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities. mBio 2020; 11:mBio.02776-19. [PMID: 31964728 PMCID: PMC6974563 DOI: 10.1128/mbio.02776-19] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities. Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.
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30
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Carini P, Delgado-Baquerizo M, Hinckley ELS, Holland-Moritz H, Brewer TE, Rue G, Vanderburgh C, McKnight D, Fierer N. Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities. mBio 2020; 11:e02776-19. [PMID: 31964728 PMCID: PMC6974563 DOI: 10.1128/mbio.02776-19 10.1128/mbio.02776-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/03/2019] [Indexed: 12/25/2023] Open
Abstract
Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.
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Affiliation(s)
- Paul Carini
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Manuel Delgado-Baquerizo
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Eve-Lyn S Hinckley
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA
- Environmental Studies Program, University of Colorado, Boulder, Colorado, USA
| | - Hannah Holland-Moritz
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Tess E Brewer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Garrett Rue
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA
| | - Caihong Vanderburgh
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Diane McKnight
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
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31
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Ramin KI, Allison SD. Bacterial Tradeoffs in Growth Rate and Extracellular Enzymes. Front Microbiol 2019; 10:2956. [PMID: 31921094 PMCID: PMC6933949 DOI: 10.3389/fmicb.2019.02956] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/09/2019] [Indexed: 11/13/2022] Open
Abstract
Like larger organisms, bacteria possess traits, or phenotypic characteristics, that influence growth and impact ecosystem processes. Still, it remains unclear how these traits are organized across bacterial lineages. Using 49 bacterial strains isolated from leaf litter in Southern California, we tested the hypothesis that bacterial growth rates trade off against extracellular enzyme investment. We also tested for phylogenetic conservation of these traits under high and low resource conditions represented, respectively, by Luria broth (LB) and a monomer-dominated medium extracted from plant litter. In support of our hypotheses, we found a negative correlation between the maximum growth rate and the total activity of carbon-, nitrogen-, and phosphorus-degrading extracellular enzymes. However, this tradeoff was only observed under high resource conditions. We also found significant phylogenetic signal in maximum growth rate and extracellular enzyme investment under high and low resource conditions. Driven by our bacterial trait data, we proposed three potential life history strategies. Resource acquisition strategists invest heavily in extracellular enzyme production. Growth strategists invest in high growth rates. Bacteria in a third category showed lower potential for enzyme production and growth, so we tentatively classified them as maintenance strategists that may perform better under conditions we did not measure. These strategies were related to bacterial phylogeny, with most growth strategists belonging to the phylum Proteobacteria and most maintenance and resource acquisition strategists belonging to the phylum Actinobacteria. By accounting for extracellular enzyme investment, our proposed life history strategies complement existing frameworks, such as the copiotroph-oligotroph continuum and Grime’s competitor-stress tolerator-ruderal triangle. Our results have biogeochemical implications because allocation to extracellular enzymes versus growth or stress tolerance can determine the fate and form of organic matter cycling through surface soil.
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Affiliation(s)
- Kelly I Ramin
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States.,Department of Earth System Science, University of California, Irvine, Irvine, CA, United States
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32
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Albright MBN, Mueller RC, Gallegos-Graves LV, Belnap J, Reed SC, Kuske CR. Interactions of Microhabitat and Time Control Grassland Bacterial and Fungal Composition. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00367] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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33
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Albright MBN, Chase AB, Martiny JBH. Experimental Evidence that Stochasticity Contributes to Bacterial Composition and Functioning in a Decomposer Community. mBio 2019; 10:e00568-19. [PMID: 30992354 PMCID: PMC6469972 DOI: 10.1128/mbio.00568-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 03/14/2019] [Indexed: 11/20/2022] Open
Abstract
Stochasticity emerging from random differences in replication, death, mutation, and dispersal is thought to alter the composition of ecological communities. However, the importance of stochastic effects remains somewhat speculative because stochasticity is not directly measured but is instead inferred from unexplained variations in beta-diversity. Here, we performed a field experiment to more directly disentangle the role of stochastic processes, environmental selection, and dispersal in the composition and functioning of a natural bacterial decomposer community in the field. To increase our ability to detect these effects, we reduced initial biological and environmental heterogeneity using replicate nylon litterbags in the field. We then applied two treatments: ambient/added precipitation and bacterial and fungal dispersal using "open" litterbags (made from 18.0-μm-pore-size mesh) ("open bacterial dispersal") versus bacterial and fungal dispersal using "closed" litterbags (made from 22.0-μm-pore-size mesh) ("closed bacterial dispersal"). After 5 months, we assayed composition and functioning by the use of three subsamples from each litterbag to disentangle stochastic effects from residual variation. Our results indicate that stochasticity via ecological drift can contribute to beta-diversity in bacterial communities. However, residual variation, which had previously been included in stochasticity estimates, accounted for more than four times as much variability. At the same time, stochastic effects on beta-diversity were not attenuated at the functional level, as measured by genetic functional potential and extracellular enzyme activity. Finally, dispersal was found to interact with precipitation availability to influence the degree to which stochasticity contributed to functional variation. Together, our results demonstrate that the ability to quantify stochastic processes is key to understanding microbial diversity and its role in ecosystem functioning.IMPORTANCE Randomness can alter the diversity and composition of ecological communities. Such stochasticity may therefore obscure the relationship between the environment and community composition and hinder our ability to predict the relationship between biodiversity and ecosystem functioning. This study investigated the role of stochastic processes, environmental selection, and dispersal in microbial composition and its functioning on an intact field community. To do this, we used a controlled and replicated experiment that was similar to that used to study population genetics in the laboratory. Our study showed that, while the stochastic effects on taxonomic composition are smaller than expected, the degree to which stochasticity contributes to variability in ecosystem processes may be much higher than previously assumed.
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Affiliation(s)
- Michaeline B N Albright
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
| | - Alexander B Chase
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
| | - Jennifer B H Martiny
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
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34
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Treseder KK, Berlemont R, Allison SD, Martiny AC. Drought increases the frequencies of fungal functional genes related to carbon and nitrogen acquisition. PLoS One 2018; 13:e0206441. [PMID: 30462680 PMCID: PMC6248904 DOI: 10.1371/journal.pone.0206441] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/14/2018] [Indexed: 12/16/2022] Open
Abstract
Although water is a critical resource for organisms, microbially-mediated processes such as decomposition and nitrogen (N) transformations can endure within ecosystems even when water is scarce. To identify underlying mechanisms, we examined the genetic potential for fungi to contribute to specific aspects of carbon (C) and N cycling in a drought manipulation in Southern California grassland. In particular, we measured the frequency of fungal functional genes encoding enzymes that break down cellulose and chitin, and take up ammonium and amino acids, in decomposing litter. Furthermore, we used "microbial cages" to reciprocally transplant litter and microbes between control and drought plots. This approach allowed us to distinguish direct effects of drought in the plot environment versus indirect effects via shifts in the microbial community or changes in litter chemistry. For every fungal functional gene we examined, the frequency of that gene within the microbial community increased significantly in drought plots compared to control plots. In contrast, when plot environment was held constant, frequencies of these fungal functional genes did not differ significantly between control-derived microbes versus drought-derived microbes, or between control-derived litter versus drought-derived litter. It appears that drought directly selects for fungi with the genetic capacity to acquire these specific C- and N-containing compounds. This genetic trait may allow fungi to take advantage of ephemeral water supplies. Altogether, proliferation of fungi with the genetic capacity for C and N acquisition may contribute to the maintenance of biogeochemical cycling under drought.
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Affiliation(s)
- Kathleen K. Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Renaud Berlemont
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, United States of America
| | - Steven D. Allison
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
- Department of Earth System Science, University of California Irvine, Irvine, California, United States of America
| | - Adam C. Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
- Department of Earth System Science, University of California Irvine, Irvine, California, United States of America
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35
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Castañeda LE, Miura T, Sánchez R, Barbosa O. Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests. PeerJ 2018; 6:e5715. [PMID: 30397540 PMCID: PMC6211267 DOI: 10.7717/peerj.5715] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/10/2018] [Indexed: 12/18/2022] Open
Abstract
Agriculture is one of the main drivers of land conversion, and agriculture practices can impact on microbial diversity. Here we characterized the phyllosphere fungal diversity associated with Carménère grapevines under conventional and organic agricultural management. We also explored the fungal diversity present in the adjacent sclerophyllous forests to explore the potential role of native forest on vineyard phyllosphere. After conducting D2 and ITS2 amplicon sequencing, we found that fungal diversity indices did not change between conventional and organic vineyards, but community structure was sensitive to the agricultural management. On the other hand, we found a high proportion of shared fungal OTUs between vineyards and native forests. In addition, both habitats had similar levels of fungal diversity despite forest samples were derived from multiple plant species. In contrast, the community structure was different in both habitats. Interestingly, the native forest had more unidentified species and unique OTUs than vineyards. Forest dominant species were Aureobasidium pullulans and Endoconidioma populi, whereas Davidiella tassiana, Didymella sp., and Alternaria eichhorniae were more abundant in vineyards. Overall, this study argues that a better understanding of the relationship native forests and agroecosystems is needed for maintaining and enhancing ecosystem services provided by natural ecosystems. Finally, knowledge of microbial communities living in the Chilean Mediterranean biome is needed for appropriate conservation management of these biomes and their classification as biodiversity hotspots.
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Affiliation(s)
- Luis E. Castañeda
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Toshiko Miura
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, Japan
- Instituto de Ecología y Biodiversidad, Santiago, Chile
| | - Roland Sánchez
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología y Biodiversidad, Santiago, Chile
| | - Olga Barbosa
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ecología y Biodiversidad, Santiago, Chile
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Chase AB, Gomez-Lunar Z, Lopez AE, Li J, Allison SD, Martiny AC, Martiny JBH. Emergence of soil bacterial ecotypes along a climate gradient. Environ Microbiol 2018; 20:4112-4126. [PMID: 30209883 DOI: 10.1111/1462-2920.14405] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/03/2018] [Accepted: 09/06/2018] [Indexed: 11/28/2022]
Abstract
The high diversity of soil bacteria is attributed to the spatial complexity of soil systems, where habitat heterogeneity promotes niche partitioning among bacterial taxa. This premise remains challenging to test, however, as it requires quantifying the traits of closely related soil bacteria and relating these traits to bacterial abundances and geographic distributions. Here, we sought to investigate whether the widespread soil taxon Curtobacterium consists of multiple coexisting ecotypes with differential geographic distributions. We isolated Curtobacterium strains from six sites along a climate gradient and assayed four functional traits that may contribute to niche partitioning in leaf litter, the top layer of soil. Our results revealed that cultured isolates separated into fine-scale genetic clusters that reflected distinct suites of phenotypic traits, denoting the existence of multiple ecotypes. We then quantified the distribution of Curtobacterium by analysing metagenomic data collected across the gradient over 18 months. Six abundant ecotypes were observed with differential abundances along the gradient, suggesting fine-scale niche partitioning. However, we could not clearly explain observed geographic distributions of ecotypes by relating their traits to environmental variables. Thus, while we can resolve soil bacterial ecotypes, the traits delineating their distinct niches in the environment remain unclear.
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Affiliation(s)
- Alexander B Chase
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Zulema Gomez-Lunar
- Department of Earth System Sciences, University of California, Irvine, California, USA
| | - Alberto E Lopez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Junhui Li
- Department of Earth System Sciences, University of California, Irvine, California, USA
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA.,Department of Earth System Sciences, University of California, Irvine, California, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA.,Department of Earth System Sciences, University of California, Irvine, California, USA
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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Lan G, Li Y, Lesueur D, Wu Z, Xie G. Seasonal changes impact soil bacterial communities in a rubber plantation on Hainan Island, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 626:826-834. [PMID: 29396343 DOI: 10.1016/j.scitotenv.2018.01.147] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 01/15/2018] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Abstract
Rubber plantations have expanded rapidly over the past 20 years in tropical Asia and their impacts on regional ecosystems have garnered much concern. While much attention has been given to the negative impacts on aboveground diversity and function, the belowground bacterial soil community has received much less attention. Here, we investigated the community composition and diversity of soil bacteria of rubber plantations on Hainan Island in south China. The goals of the study were to describe changes in bacterial compositions and diversity across seasons. We found that seasonality defined by differences in rainfall amount strongly influenced bacterial communities. At both the Phylum and Family levels, we found significant differences in the total number of taxa, as well as the composition of the community as a function of season. Diversity of soil samples in the dry-rainy season was highest of three seasons, suggesting that bacterial structure was more sensitive in alternate periods of season. Diversity in the rainy season was substantial lower than in dry season. Results from a redundancy analysis showed that seasonal changes explained the largest part (31.9%) of the total variance of bacterial community composition. In conclusion, seasonal change had the greatest influence on bacterial communities, which overshadowed the effects of soil nutrient as well as other factors, and controls the bacterial communities in soils of RP in tropical region of Hainan.
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Affiliation(s)
- Guoyu Lan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou City, Hainan Province 571737, PR China; Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 88 Xuefu Road, Kunming 650223, PR China; Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Danzhou City, Hainan Province 571737, PR China.
| | - Yuwu Li
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 88 Xuefu Road, Kunming 650223, PR China.
| | - Didier Lesueur
- Eco & Sols, University Montpellier, CIRAD, Montpellier, France; CIRAD, UMR ECO & SOLS, CIAT-Asia, Hanoi, Vietnam; Deakin University, Melbourne, Australia
| | - Zhixiang Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou City, Hainan Province 571737, PR China; Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Danzhou City, Hainan Province 571737, PR China
| | - Guishui Xie
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou City, Hainan Province 571737, PR China; Danzhou Investigation & Experiment Station of Tropical Crops, Ministry of Agriculture, Danzhou City, Hainan Province 571737, PR China
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38
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Guo X, Zhou X, Hale L, Yuan M, Feng J, Ning D, Shi Z, Qin Y, Liu F, Wu L, He Z, Van Nostrand JD, Liu X, Luo Y, Tiedje JM, Zhou J. Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass. Front Microbiol 2018; 9:954. [PMID: 29904372 PMCID: PMC5990867 DOI: 10.3389/fmicb.2018.00954] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/24/2018] [Indexed: 11/13/2022] Open
Abstract
Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010-2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P < 0.05) increased root and microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P < 0.05) changed by clipping. Clipping significantly (P < 0.05) increased the abundances of labile carbon (C) degrading genes. More importantly, the abundances of recalcitrant C degrading genes were consistently and significantly (P < 0.05) increased by clipping in the last 2 years, which could accelerate recalcitrant C degradation and weaken long-term soil carbon stability. Furthermore, genes involved in nutrient-cycling processes including nitrogen cycling and phosphorus utilization were also significantly increased by clipping. The shifts of microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices.
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Affiliation(s)
- Xue Guo
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Xishu Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Lauren Hale
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Mengting Yuan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Jiajie Feng
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Zhou Shi
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Yujia Qin
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Feifei Liu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Joy D. Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, United States
- Earth and Environmental Science, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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39
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Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1375-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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40
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Abstract
Microbial ecology has been transformed by the advent of high-throughput marker gene and metagenomic sequencing methods. These tools provide expansive descriptions of microbial communities, but the descriptions are framed in terms of molecular objects, such as 97% ribosomal operational taxonomic units (OTUs), rather than biological objects, such as species. A recent study by A. B. Chase and colleagues (mBio 8:e01809-17, 2017, https://doi.org/10.1128/mBio.01809-17) explores the so-called microdiversity within the Curtobacterium OTU, the most abundant OTU in a leaf litter community. Perhaps unsurprisingly, they find that some important ecologic traits, such as drought response, are coherent within the OTU, but that others vary significantly. Here we discuss their findings in relation to the more general issue of how molecular tools can be effectively used to study microbial ecology. We specifically note the need for investigators to choose the right molecular methods for their biological problem, as nature does not respect the limitations and conventions associated with our methods.
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41
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Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits. mBio 2017; 8:mBio.01809-17. [PMID: 29138307 PMCID: PMC5686540 DOI: 10.1128/mbio.01809-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs) defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium, Curtobacterium, which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collected in situ over 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU. The response of Curtobacterium to seasonal variability and the global change manipulations, specifically an increase in relative abundance under decreased water availability, appeared to be conserved across six Curtobacterium lineages identified at this site. Genomic and physiological analyses in the lab revealed that degradation of abundant polymeric carbohydrates within leaf litter, cellulose and xylan, is nearly universal across the genus, which may contribute to its high abundance in grassland leaf litter. However, the degree of carbohydrate utilization and temperature preference for this degradation varied greatly among clades. Overall, we find that traits within Curtobacterium are conserved at different phylogenetic depths. We speculate that similar to bacteria in marine systems, diverse microbes within this taxon may be structured in distinct ecotypes that are key to understanding Curtobacterium abundance and distribution in the environment. Despite the plummeting costs of sequencing, characterizing the fine-scale genetic diversity of a microbial community—and interpreting its functional importance—remains a challenge. Indeed, most studies, particularly studies of soil, assess community composition at a broad genetic level by classifying diversity into taxa (OTUs) defined by 16S rRNA sequence similarity. However, these classifications potentially obscure variation in traits that result in fine-scale ecological differentiation among closely related strains. Here, we investigated “microdiversity” in a highly diverse and poorly characterized soil system (leaf litter in a southern Californian grassland). We focused on the most abundant bacterium, Curtobacterium, which by standard methods is grouped into only one OTU. We find that the degree of carbohydrate usage and temperature preference vary within the OTU, whereas its responses to changes in precipitation are relatively uniform. These results suggest that microdiversity may be key to understanding how soil bacterial diversity is linked to ecosystem functioning.
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42
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Dispersal alters bacterial diversity and composition in a natural community. ISME JOURNAL 2017; 12:296-299. [PMID: 29053150 DOI: 10.1038/ismej.2017.161] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 08/04/2017] [Accepted: 08/22/2017] [Indexed: 11/08/2022]
Abstract
Dispersal is central to the evolution and maintenance of microbial diversity. Quantifying microbial dispersal and its role in shaping communities remains a challenge, however. Here, we manipulated a bacterial community's dispersal rate in a grassland ecosystem and test whether this altered diversity and composition. We constructed bags of two nylon mesh sizes that allowed more or less bacterial movement and filled them with an edible or inedible substrate, irradiated plant litter or nylon sheets. We measured changes in bacterial abundance (using flow cytometry) and composition (using 16S amplicon sequencing) in the bags weekly over 5 months. The dispersal treatment altered bacterial colonization rates and led to differences in the abundance, richness, evenness and composition of communities. Overall, the study demonstrates that dispersal influences the assembly of this natural bacterial community.
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43
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Lewin GR, Carlos C, Chevrette MG, Horn HA, McDonald BR, Stankey RJ, Fox BG, Currie CR. Evolution and Ecology of Actinobacteria and Their Bioenergy Applications. Annu Rev Microbiol 2017; 70:235-54. [PMID: 27607553 DOI: 10.1146/annurev-micro-102215-095748] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.
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Affiliation(s)
- Gina R Lewin
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Marc G Chevrette
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Heidi A Horn
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706;
| | - Bradon R McDonald
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Robert J Stankey
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Brian G Fox
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726.,Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
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Gravuer K, Eskelinen A. Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities. Front Microbiol 2017; 8:1271. [PMID: 28744266 PMCID: PMC5504382 DOI: 10.3389/fmicb.2017.01271] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/23/2017] [Indexed: 02/01/2023] Open
Abstract
Microbial traits related to ecological responses and functions could provide a common currency facilitating synthesis and prediction; however, such traits are difficult to measure directly for all taxa in environmental samples. Past efforts to estimate trait values based on phylogenetic relationships have not always distinguished between traits with high and low phylogenetic conservatism, limiting reliability, especially in poorly known environments, such as soil. Using updated reference trees and phylogenetic relationships, we estimated two phylogenetically conserved traits hypothesized to be ecologically important from DNA sequences of the 16S rRNA gene from soil bacterial and archaeal communities. We sampled these communities from an environmental change experiment in California grassland applying factorial addition of late-season precipitation and soil nutrients to multiple soil types for 3 years prior to sampling. Estimated traits were rRNA gene copy number, which contributes to how rapidly a microbe can respond to an increase in resources and may be related to its maximum growth rate, and genome size, which suggests the breadth of environmental and substrate conditions in which a microbe can thrive. Nutrient addition increased community-weighted mean estimated rRNA gene copy number and marginally increased estimated genome size, whereas precipitation addition decreased these community means for both estimated traits. The effects of both treatments on both traits were associated with soil properties, such as ammonium, available phosphorus, and pH. Estimated trait responses within several phyla were opposite to the community mean response, indicating that microbial responses, although largely consistent among soil types, were not uniform across the tree of life. Our results show that phylogenetic estimation of microbial traits can provide insight into how microbial ecological strategies interact with environmental changes. The method could easily be applied to any of the thousands of existing 16S rRNA sequence data sets and offers potential to improve our understanding of how microbial communities mediate ecosystem function responses to global changes.
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Affiliation(s)
- Kelly Gravuer
- Graduate Group in Ecology, Department of Plant Sciences, University of California, DavisDavis, CA, United States
| | - Anu Eskelinen
- Department of Physiological Diversity, Helmholtz Center for Environmental Research-UFZLeipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany.,Department of Ecology, University of OuluOulu, Finland.,Department of Environmental Science and Policy, University of California, DavisDavis, CA, United States
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45
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Effects of different nitrogen additions on soil microbial communities in different seasons in a boreal forest. Ecosphere 2017. [DOI: 10.1002/ecs2.1879] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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46
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Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration. Appl Environ Microbiol 2017; 83:AEM.00966-17. [PMID: 28476769 DOI: 10.1128/aem.00966-17] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 01/06/2023] Open
Abstract
Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, β-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping β-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial β-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities.IMPORTANCE Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery patterns improves the understanding of how different components of the soil microbiota respond to ecosystem recovery. In this study, we highlight key differences between soil bacteria and fungi during the restoration of reclaimed mine soils in the form of long-term diversity patterns, intra-annual variability, and potential interaction networks. Cooccurrence networks revealed increasingly complex bacterial community interactions during recovery, in contrast to much simpler and more isolated fungal network patterns. This study compares bacterial and fungal cooccurrence networks and reveals cooccurrences persisting through successional ages.
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47
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Dolan KL, Peña J, Allison SD, Martiny JBH. Phylogenetic conservation of substrate use specialization in leaf litter bacteria. PLoS One 2017; 12:e0174472. [PMID: 28358894 PMCID: PMC5373539 DOI: 10.1371/journal.pone.0174472] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/09/2017] [Indexed: 11/20/2022] Open
Abstract
Environmental change will influence the ecosystem processes regulated by microbial communities, including leaf litter decomposition. To assess how microbial communities and their functioning might respond to increases in temperature, we quantified the distribution of traits related to carbon substrate utilization and temperature sensitivity in leaf litter bacteria isolated from a natural grassland ecosystem in Southern California. The isolates varied substantially in their carbon substrate use, as well as their response to temperature change. To better predict the functioning and responses in natural communities, we also examined if the functional and response traits were phylogenetically patterned or correlated with one another. We found that the distribution of functional traits displayed a phylogenetic pattern, but the sensitivity of the traits to changes in temperature did not. We also did not detect any correlations between carbon substrate use and sensitivity to changes in temperature. Together, these results suggest that information about microbial composition may provide insights to predicting ecosystem function under one temperature, but that these relationships may not hold under new temperature conditions.
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Affiliation(s)
- Kristin L. Dolan
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, United States of America
- * E-mail:
| | - Jeniffer Peña
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, United States of America
| | - Steven D. Allison
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, United States of America
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, United States of America
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48
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Zhang Y, Dong S, Gao Q, Liu S, Ganjurjav H, Wang X, Su X, Wu X. Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes. Sci Rep 2017; 7:43077. [PMID: 28262753 PMCID: PMC5338028 DOI: 10.1038/srep43077] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/19/2017] [Indexed: 01/11/2023] Open
Abstract
To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH4-N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands. Soil microbial biomass carbon and phosphorus along with the sucrase and phosphatase activities were generally stable under different treatments. Soil NO3-N, available phosphorus, urease activity and microbial biomass nitrogen were increased by overgrazing in the cultivated grassland. Soil bacterial diversity was positively correlated with, while soil fungal diversity negatively with soil microbial biomass and enzyme activities. Soil bacterial diversity was negatively correlated with, while soil fungal diversity positively with soil available nutrients. Our findings indicated soil bacteria and fungi played different roles in affecting soil nutrients and microbiological activities that might provide an important implication to understand why soil biochemistry was generally stable under environmental changes in alpine grassland ecosystems.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
- National Plateau Wetland Research Center, Southwest Forestry University, Kunming, 650224, China
| | - Shikui Dong
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qingzhu Gao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shiliang Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Hasbagan Ganjurjav
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuexia Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xukun Su
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xiaoyu Wu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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Lucas J, Bill B, Stevenson B, Kaspari M. The microbiome of the ant‐built home: the microbial communities of a tropical arboreal ant and its nest. Ecosphere 2017. [DOI: 10.1002/ecs2.1639] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Jane Lucas
- Department of Biology Graduate Program in Ecology and Evolutionary Biology University of Oklahoma Norman Oklahoma 73019 USA
| | - Brian Bill
- Department of Microbiology and Plant Biology Graduate Program in Ecology and Evolutionary Biology University of Oklahoma Norman Oklahoma 73019 USA
| | - Bradley Stevenson
- Department of Microbiology and Plant Biology Graduate Program in Ecology and Evolutionary Biology University of Oklahoma Norman Oklahoma 73019 USA
| | - Michael Kaspari
- Department of Biology Graduate Program in Ecology and Evolutionary Biology University of Oklahoma Norman Oklahoma 73019 USA
- Smithsonian Tropical Research Institute Apartado 2072 Balboa Panamá
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Martiny JBH, Martiny AC, Weihe C, Lu Y, Berlemont R, Brodie EL, Goulden ML, Treseder KK, Allison SD. Microbial legacies alter decomposition in response to simulated global change. THE ISME JOURNAL 2017; 11:490-499. [PMID: 27740610 PMCID: PMC5270563 DOI: 10.1038/ismej.2016.122] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/11/2016] [Accepted: 08/05/2016] [Indexed: 01/19/2023]
Abstract
Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we decoupled the legacies of abiotic parameters versus that of the microbial community itself. After one rainy season, more variation in fungal composition could be explained by the original microbial inoculum than the litterbag environment (18% versus 5.5% of total variation). This compositional legacy persisted for 3 years, when 6% of the variability in fungal composition was still explained by the microbial origin. In contrast, bacterial composition was generally more resilient than fungal composition. Microbial functioning (measured as decomposition rate) was not immediately resilient to the global change manipulations; decomposition depended on both the contemporary environment and rainfall the year prior. Finally, using metagenomic sequencing, we showed that changes in precipitation, but not nitrogen availability, altered the potential for bacterial carbohydrate degradation, suggesting why the functional consequences of the two experiments may have differed. Predictions of how terrestrial ecosystem processes respond to environmental change may thus be improved by considering the legacies of microbial communities.
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Affiliation(s)
- Jennifer BH Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Claudia Weihe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Ying Lu
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Renaud Berlemont
- Department of Earth System Science, University of California, Irvine, CA, USA
- Department of Biology, California State University, Long Beach, CA, USA
| | - Eoin L Brodie
- Ecology Department, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Michael L Goulden
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
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