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Malard LA, Bergk-Pinto B, Layton R, Vogel TM, Larose C, Pearce DA. Snow Microorganisms Colonise Arctic Soils Following Snow Melt. MICROBIAL ECOLOGY 2023; 86:1661-1675. [PMID: 36939866 PMCID: PMC10497451 DOI: 10.1007/s00248-023-02204-y] [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: 05/21/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Arctic soils are constantly subjected to microbial invasion from either airborne, marine, or animal sources, which may impact local microbial communities and ecosystem functioning. However, in winter, Arctic soils are isolated from outside sources other than snow, which is the sole source of microorganisms. Successful colonisation of soil by snow microorganisms depends on the ability to survive and compete of both, the invading and resident community. Using shallow shotgun metagenome sequencing and amplicon sequencing, this study monitored snow and soil microbial communities throughout snow melt to investigate the colonisation process of Arctic soils. Microbial colonisation likely occurred as all the characteristics of successful colonisation were observed. The colonising microorganisms originating from the snow were already adapted to the local environmental conditions and were subsequently subjected to many similar conditions in the Arctic soil. Furthermore, competition-related genes (e.g. motility and virulence) increased in snow samples as the snow melted. Overall, one hundred potentially successful colonisers were identified in the soil and, thus, demonstrated the deposition and growth of snow microorganisms in soils during melt.
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Affiliation(s)
- Lucie A Malard
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-Upon-Tyne, NE1 8ST, UK.
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Benoit Bergk-Pinto
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
- BioIT, TAG (Transversal Activities in Applied Genomics) Sciensano, 1050, Brussels, Belgium
| | - Rose Layton
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, CNRS, University of Lyon, Lyon, France
| | - David A Pearce
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-Upon-Tyne, NE1 8ST, UK.
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52
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Malard LA, Guisan A. Into the microbial niche. Trends Ecol Evol 2023; 38:936-945. [PMID: 37236880 DOI: 10.1016/j.tree.2023.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023]
Abstract
The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.
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Affiliation(s)
- Lucie A Malard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
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53
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Affiliation(s)
| | | | | | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Tomislav Cernava
- University of Southampton, Faculty of Environmental and Life Sciences, Southampton, United Kingdom
| | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | | | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pedro Lebre
- University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- University of Pretoria, Pretoria, South Africa
| | - Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | - Lidia Markiewicz
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Department of Immunology and Food Microbiology, Olsztyn, Poland
| | - Annelein Meisner
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Inga Sarand
- Tallinn University of Technology, Department of Chemistry and Biotechnology, Tallinn, Estonia
| | | | | | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Leo van Overbeek
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - S. J. Liu
- Chinese Academy of Sciences, Institute of Microbiology, Beijing, China
| | - Matthew Ryan
- Genetic Resources Collection, CABI, Egham, United Kingdom
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
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Shibasaki S, Mitri S. A spatially structured mathematical model of the gut microbiome reveals factors that increase community stability. iScience 2023; 26:107499. [PMID: 37670791 PMCID: PMC10475486 DOI: 10.1016/j.isci.2023.107499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/11/2023] [Accepted: 07/26/2023] [Indexed: 09/07/2023] Open
Abstract
Given the importance of gut microbial communities for human health, we may want to ensure their stability in terms of species composition and function. Here, we built a mathematical model of a simplified gut composed of two connected patches where species and metabolites can flow from an upstream patch, allowing upstream species to affect downstream species' growth. First, we found that communities in our model are more stable if they assemble through species invasion over time compared to combining a set of species from the start. Second, downstream communities are more stable when species invade the downstream patch less frequently than the upstream patch. Finally, upstream species that have positive effects on downstream species can further increase downstream community stability. Despite it being quite abstract, our model may inform future research on designing more stable microbial communities or increasing the stability of existing ones.
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Affiliation(s)
- Shota Shibasaki
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Lasa AV, Fernández-González AJ, Villadas PJ, Cobo-Díaz JF, Fernández-López M. Bacterial inoculation of Quercus pyrenaica trees alters co-occurrence patterns but not the composition of the rhizosphere bacteriome in wild conditions. Environ Microbiol 2023; 25:1747-1761. [PMID: 37186411 DOI: 10.1111/1462-2920.16388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/18/2023] [Indexed: 05/17/2023]
Abstract
Quercus pyrenaica is a woody species of high landscape value, however, its forests show an advanced state of degradation in the Iberian Peninsula. Afforestation typically has low success, thus, it is necessary to improve the fitness of oaks plantlets to be transplanted, for instance, by inoculating beneficial microorganisms. In adding microorganisms to ecosystems, there must be balanced efficacy with potential effects on native microbial communities. We addressed changes in diversity, richness, composition and co-occurrence networks of prokaryotic communities in the rhizosphere of inoculated and control trees outplanted to three different sites located in the Sierra Nevada National and Natural Park (Spain). After 18 months in wild conditions, we did not detect changes due to the inoculation in the richness, diversity and structure in none of the sites. However, we observed an increase in the complexity of the co-occurrence networks in two experimental areas. Modularization of the networks changed as a result of the inoculation, although the sense of the change depended on the site. Although it was impossible to unravel the effect of bacterial inoculation, our results highlighted that inoculation alters the association of rhizosphere bacteria without entailing other changes, so networks should be analysed prior to inoculating the plantlets.
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Affiliation(s)
- Ana V Lasa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | | | - Pablo J Villadas
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Faculty of Veterinary, Universidad de León, León, Spain
| | - M Fernández-López
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, Granada, Spain
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Larke JA, Heiss BE, Ehrlich AM, Taft DH, Raybould HE, Mills DA, Slupsky CM. Milk oligosaccharide-driven persistence of Bifidobacterium pseudocatenulatum modulates local and systemic microbial metabolites upon synbiotic treatment in conventionally colonized mice. MICROBIOME 2023; 11:194. [PMID: 37635250 PMCID: PMC10463478 DOI: 10.1186/s40168-023-01624-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/14/2023] [Indexed: 08/29/2023]
Abstract
BACKGROUND Bifidobacteria represent an important gut commensal in humans, particularly during initial microbiome assembly in the first year of life. Enrichment of Bifidobacterium is mediated though the utilization of human milk oligosaccharides (HMOs), as several human-adapted species have dedicated genomic loci for transport and metabolism of these glycans. This results in the release of fermentation products into the gut lumen which may offer physiological benefits to the host. Synbiotic pairing of probiotic species with a cognate prebiotic delivers a competitive advantage, as the prebiotic provides a nutrient niche. METHODS To determine the fitness advantage and metabolic characteristics of an HMO-catabolizing Bifidobacterium strain in the presence or absence of 2'-fucosyllactose (2'-FL), conventionally colonized mice were gavaged with either Bifidobacterium pseudocatenulatum MP80 (B.p. MP80) (as the probiotic) or saline during the first 3 days of the experiment and received water or water containing 2'-FL (as the prebiotic) throughout the study. RESULTS 16S rRNA gene sequencing revealed that mice provided only B.p. MP80 were observed to have a similar microbiota composition as control mice throughout the experiment with a consistently low proportion of Bifidobacteriaceae present. Using 1H NMR spectroscopy, similar metabolic profiles of gut luminal contents and serum were observed between the control and B.p. MP80 group. Conversely, synbiotic supplemented mice exhibited dramatic shifts in their community structure across time with an overall increased, yet variable, proportion of Bifidobacteriaceae following oral inoculation. Parsing the synbiotic group into high and moderate bifidobacterial persistence based on the median proportion of Bifidobacteriaceae, significant differences in gut microbial diversity and metabolite profiles were observed. Notably, metabolites associated with the fermentation of 2'-FL by bifidobacteria were significantly greater in mice with a high proportion of Bifidobacteriaceae in the gut suggesting metabolite production scales with population density. Moreover, 1,2-propanediol, a fucose fermentation product, was only observed in the liver and brain of mice harboring high proportions of Bifidobacteriaceae. CONCLUSIONS This study reinforces that the colonization of the gut with a commensal microorganism does not guarantee a specific functional output. Video Abstract.
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Affiliation(s)
- Jules A Larke
- Department of Nutrition, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Britta E Heiss
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Amy M Ehrlich
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, , Davis, CA, USA
| | - Diana H Taft
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Helen E Raybould
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, , Davis, CA, USA
| | - David A Mills
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
| | - Carolyn M Slupsky
- Department of Nutrition, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
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57
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Qin H, Cai R, Wang Y, Deng X, Chen J, Xing J. Intensive management facilitates bacterial invasion on soil microbial community. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 340:117963. [PMID: 37105104 DOI: 10.1016/j.jenvman.2023.117963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 05/12/2023]
Abstract
Intensive management has greatly altered natural forests, especially forests around the world are increasingly being converted into economic plantations. Soil microbiota are critical for community functions in all ecosystems, but the effects of microbial disturbance during economic plantation remain unclear. Here, we used Escherichia coli O157:H7, a model pathogenic species for bacterial invasion, to assess the invasion impacts on the soil microbial community under intensive management. The E. coli invasion was tracked for 135 days to explore the instant and legacy impacts on the resident community. Our results showed that bamboo economic plantations altered soil abiotic and biotic properties, especially increasing pH and community diversity. Higher pH in bamboo soils resulted in longer pathogen survivals than in natural hardwood soils, indicating that pathogen suppression during intensive management should arouse our attention. A longer invasion legacy effect on the resident community (P < 0.05) were found in bamboo soils underlines the need to quantify the soil resilience even when the invasion was unsuccessful. Deterministic processes drove community assembly in bamboo plantations, and this selection acted more strongly during by E. coli invasion than in hardwood soils. We also showed more associated co-occurrence patterns in bamboo plantations, suggesting more complex potential interactions within the microbial community. Apart from community structure, community functions are also strongly related to the resident species associated with invaders. These findings provide new perspectives to understand intensive management facilitates the bacterial invasion, and the impacts would leave potential risks on environmental and human health.
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Affiliation(s)
- Hua Qin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Ruihang Cai
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 310021, China
| | - Yanan Wang
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 310021, China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junhui Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jiajia Xing
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China.
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58
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Xu W, Sun T, Du J, Jin S, Zhang Y, Bai G, Li W, Yin D. Structure and ecological function of the soil microbiome associated with 'Sanghuang' mushrooms suffering from fungal diseases. BMC Microbiol 2023; 23:218. [PMID: 37573330 PMCID: PMC10422728 DOI: 10.1186/s12866-023-02965-z] [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: 01/02/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023] Open
Abstract
BACKGROUND The most serious challenges in medicinal 'Sanghuang' mushroom production are the fungal diseases caused by various molds. Application of biological agents has been regarded as a potential crop disease management strategy. Here, the soil microbiome associated with 'Sanghuang' mushroom affected by fungal diseases grown under field cultivation (FC) and hanging cultivation (HC) was characterized using culture-dependent and culture-independent methods. RESULTS A total of 12,525 operational taxonomic units (OTUs) and 168 pure cultures were obtained using high-throughput sequencing and a culture-dependent method, respectively. From high-throughput sequencing, we found that HC samples had more OTUs, higher α-diversity, and greater microbial community complexity than FC samples. Analysis of β-diversity divided the soil microbes into two groups according to cultivation mode. Basidiomycota (48.6%) and Ascomycota (46.5%) were the two dominant fungal phyla in FC samples, with the representative genera Trichoderma (56.3%), Coprinellus (29.4%) and Discosia (4.8%), while only the phylum Ascomycota (84.5%) was predominant in HC samples, with the representative genera Discosia (34.0%), Trichoderma (30.2%), Penicillium (14.9%), and Aspergillus (7.8%). Notably, Trichoderma was predominant in both the culture-independent and culture-dependent analyses, with Trichoderma sp. FZ0005 showing high host pathogenicity. Among the 87 culturable bacteria, 15 exhibited varying extents of antifungal activity against Trichoderma sp. FZ0005, with three strains of Bacillus spp. (HX0037, HX0016, and HX0039) showing outstanding antifungal capacity. CONCLUSIONS Overall, our results suggest that Trichoderma is the major causal agent of 'Sanghuang' fungal diseases and that Bacillus strains may be used as biocontrol agents in 'Sanghuang' cultivation.
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Affiliation(s)
- Weifang Xu
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
| | - Tao Sun
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
| | - Jiahui Du
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Shuqing Jin
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Ying Zhang
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Guofa Bai
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Wanyu Li
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Dengke Yin
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
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Schlatter DC, Gamble JD, Castle S, Rogers J, Wilson M. Abiotic and Biotic Drivers of Soil Fungal Communities in Response to Dairy Manure Amendment. Appl Environ Microbiol 2023; 89:e0193122. [PMID: 37212685 PMCID: PMC10304672 DOI: 10.1128/aem.01931-22] [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] [Received: 11/15/2022] [Accepted: 04/24/2023] [Indexed: 05/23/2023] Open
Abstract
Modern agriculture often relies on large inputs of synthetic fertilizers to maximize crop yield potential, yet their intensive use has led to nutrient losses and impaired soil health. Alternatively, manure amendments provide plant available nutrients, build organic carbon, and enhance soil health. However, we lack a clear understanding of how consistently manure impacts fungal communities, the mechanisms via which manure impacts soil fungi, and the fate of manure-borne fungi in soils. We assembled soil microcosms using five soils to investigate how manure amendments impact fungal communities over a 60-day incubation. Further, we used autoclaving treatments of soils and manure to determine if observed changes in soil fungal communities were due to abiotic or biotic properties, and if indigenous soil communities constrained colonization of manure-borne fungi. We found that manure amended soil fungal communities diverged from nonamended communities over time, often in concert with a reduction in diversity. Fungal communities responded to live and autoclaved manure in a similar manner, suggesting that abiotic forces are primarily responsible for the observed dynamics. Finally, manure-borne fungi declined quickly in both live and autoclaved soil, indicating that the soil environment is unsuitable for their survival. IMPORTANCE Manure amendments in agricultural systems can impact soil microbial communities via supplying growth substrates for indigenous microbes or by introducing manure-borne taxa. This study explores the consistency of these impacts on soil fungal communities and the relative importance of abiotic and biotic drivers across distinct soils. Different fungal taxa responded to manure among distinct soils, and shifts in soil fungal communities were driven largely by abiotic factors, rather than introduced microbes. This work demonstrates that manure may have inconsistent impacts on indigenous soil fungi, and that abiotic properties of soils render them largely resistant to invasion by manure-borne fungi.
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Affiliation(s)
| | - Joshua D. Gamble
- USDA-ARS Plant Science Research Unit, Saint Paul, Minnesota, USA
| | - Sarah Castle
- USDA-ARS Plant Science Research Unit, Saint Paul, Minnesota, USA
| | - Julia Rogers
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
| | - Melissa Wilson
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
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Dai Y, Li J, Yang X, Wang S, Zhao X, Wang Y, Zhang D, Luo C, Zhang G. New insight into the mechanisms of autochthonous fungal bioaugmentation of phenanthrene in petroleum contaminated soil by stable isotope probing. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131271. [PMID: 36989785 DOI: 10.1016/j.jhazmat.2023.131271] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 05/03/2023]
Abstract
Autochthonous fungal bioaugmentation (AFB) is considered a reliable bioremediation approach for polycyclic aromatic hydrocarbon (PAH) contamination, but little is known about its mechanisms in contaminated soils. Here, a microcosm experiment was performed to explore the AFB mechanisms associated with two highly efficient phenanthrene degrading agents of fungi (with laccase-producing Scedosporium aurantiacum GIG-3 and non-laccase-producing Aspergillus fumigatus LJD-29), using stable-isotope-probing (SIP) and high-throughput sequencing. The results showed that each fungus markedly improved phenanthrene removal, and microcosms with both fungi exhibited the best phenanthrene removal performance among all microcosms. Additionally, AFB markedly shifted the composition of the microbial community, particularly the phenanthrene-degrading bacterial taxa. Interestingly, based on SIP results, strains GIG-3 and LJD-29 did not assimilate phenanthrene directly during AFB, but instead played key roles in the preliminary decomposition of phenanthrene though secretion of different extracellular enzymes to oxidize the benzene ring (GIG-3 bioaugmentation with laccase, and LJD-29 bioaugmentation with manganese and lignin peroxidases). In addition, all functional degraders directly involved in phenanthrene assimilation were indigenous bacteria, while native fungi rarely participated in the direct phenanthrene mineralization. Our findings provide a new mechanism of AFB with multiple fungi, and support AFB as a promising strategy for the in situ bioremediation of PAH-contaminated soil.
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Affiliation(s)
- Yeliang Dai
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Xiumin Yang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Shuang Wang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xuan Zhao
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yujie Wang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
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Long J, Zhou D, Wang J, Huang B, Luo Y, Zhang G, Liu Z, Lei M. Repeated inoculation of antimony resistant bacterium reduces antimony accumulation in rice plants. CHEMOSPHERE 2023; 327:138335. [PMID: 36948256 DOI: 10.1016/j.chemosphere.2023.138335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
Applying beneficial bacteria in rice rhizosphere to manage heavy metal behaviour in soil-plant system is a promising strategy. However, colonization/domination of exogenous bacteria in rhizosphere soils remains a challenge. In this study, a bacterium Ochrobactrum anthropi, which showed the potential of transforming soluble SbIII into Sb2O3 mineral, was repeatedly inoculated into the rice rhizosphere weekly throughout the rice growth period, and the colonization of this bacterium in rice rhizosphere soils and its effect on Sb accumulation in rice plants were investigated. Results showed that repeated inoculants changed the native bacterial community in rhizosphere soils in comparison with the control, but the inoculated O. anthropi was not identified as an abundant species. With weekly inoculation, the decrease in Sb in rice roots and straws was maintained throughout the rice growth period, with decrease percentages ranging from 36 to 49% and 33-35%. In addition, decrease percentages of Sb in husks and grains at the maturing stage obtained 34 and 37%, respectively. Furthermore, the XRD identified the formation of valentinite (Sb2O3) on rice root in inoculation treatment, and the decrease percentages in aqueous SbIII in rhizosphere were 53-100% through the growth period. It demonstrated that weekly inoculants performed their temporary activity of valentinite formation, and reduced Sb accumulation in rice plants efficiently. This study suggests that regardless of successful colonization, repeated inoculation of beneficial bacteria is an option to facilitate the positive effects of inoculated bacteria in the management of heavy metal behaviour.
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Affiliation(s)
- Jiumei Long
- Hunan Key Laboratory for Conservation & Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences, Hengyang Normal University, Hengyang, 421008, PR China
| | - Dongsheng Zhou
- Hunan Key Laboratory for Conservation & Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences, Hengyang Normal University, Hengyang, 421008, PR China
| | - Jing Wang
- Hunan Key Laboratory for Conservation & Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences, Hengyang Normal University, Hengyang, 421008, PR China
| | - Binyan Huang
- Hunan Key Laboratory for Conservation & Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences, Hengyang Normal University, Hengyang, 421008, PR China
| | - Yuanlai Luo
- Hunan Key Laboratory for Conservation & Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences, Hengyang Normal University, Hengyang, 421008, PR China
| | - Guocheng Zhang
- Hunan Key Laboratory for Conservation & Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences, Hengyang Normal University, Hengyang, 421008, PR China
| | - Zui Liu
- Hunan Key Laboratory for Conservation & Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences, Hengyang Normal University, Hengyang, 421008, PR China
| | - Ming Lei
- Hunan Engineering Research Center for Safe & High-Efficient Utilization of Heavy Metal Pollution Farmland, College of Resource & Environment, Hunan Agricultural University, Changsha, 410128, PR China.
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Herpell JB, Alickovic A, Diallo B, Schindler F, Weckwerth W. Phyllosphere symbiont promotes plant growth through ACC deaminase production. THE ISME JOURNAL 2023:10.1038/s41396-023-01428-7. [PMID: 37264153 DOI: 10.1038/s41396-023-01428-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
Plant growth promoting bacteria can confer resistance to various types of stress and increase agricultural yields. The mechanisms they employ are diverse. One of the most important genes associated with the increase in plant biomass and stress resistance is acdS, which encodes a 1-aminocyclopropane-1-carboxylate- or ACC-deaminase. The non-proteinogenic amino acid ACC is the precursor and means of long-distance transport of ethylene, a plant hormone associated with growth arrest. Expression of acdS reduces stress induced ethylene levels and the enzyme is abundant in rhizosphere colonizers. Whether ACC hydrolysis plays a role in the phyllosphere, both as assembly cue and in growth promotion, remains unclear. Here we show that Paraburkholderia dioscoreae Msb3, a yam phyllosphere symbiont, colonizes the tomato phyllosphere and promotes plant growth by action of its ACC deaminase. We found that acdS is required for improved plant growth but not for efficient leaf colonization. Strain Msb3 readily proliferates on the leaf surface of tomato, only occasionally spreading to the leaf endosphere through stomata. The strain can also colonize the soil or medium around the roots but only spreads into the root if the plant is wounded. Our results indicate that the degradation of ACC is not just an important trait of plant growth promoting rhizobacteria but also one of leaf dwelling phyllosphere bacteria. Manipulation of the leaf microbiota by means of spray inoculation may be more easily achieved than that of the soil. Therefore, the application of ACC deaminase containing bacteria to the phyllosphere may be a promising strategy to increasing plant stress resistance, pathogen control, and harvest yields.
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Affiliation(s)
- Johannes B Herpell
- Molecular Systems Biology Division, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Ajtena Alickovic
- Molecular Systems Biology Division, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Bocar Diallo
- Molecular Systems Biology Division, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Florian Schindler
- Molecular Systems Biology Division, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology Division, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
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63
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Nakandalage R, Guan LL, Malmuthuge N. Microbial Interventions to Improve Neonatal Gut Health. Microorganisms 2023; 11:1328. [PMID: 37317302 DOI: 10.3390/microorganisms11051328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/04/2023] [Accepted: 05/16/2023] [Indexed: 06/16/2023] Open
Abstract
The diverse pioneer microbial community colonizing the mammalian gastrointestinal tract is critical for the developing immune system. Gut microbial communities of neonates can be affected by various internal and external factors, resulting in microbial dysbiosis. Microbial dysbiosis during early life affects gut homeostasis by changing metabolic, physiological, and immunological status, which increases susceptibility to neonatal infections and long-term pathologies. Early life is crucial for the establishment of microbiota and the development of the host immune system. Therefore, it provides a window of opportunity to reverse microbial dysbiosis with a positive impact on host health. Recent attempts to use microbial interventions during early life have successfully reversed dysbiotic gut microbial communities in neonates. However, interventions with persistent effects on microbiota and host health are still limited. This review will critically discuss microbial interventions, modulatory mechanisms, their limitations, and gaps in knowledge to understand their roles in improving neonatal gut health.
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Affiliation(s)
- Ranga Nakandalage
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Lethbridge Research and Development Center, Agriculture Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Nilusha Malmuthuge
- Lethbridge Research and Development Center, Agriculture Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
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64
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Schroer WF, Kepner HE, Uchimiya M, Mejia C, Rodriguez LT, Reisch CR, Moran MA. Functional annotation and importance of marine bacterial transporters of plankton exometabolites. ISME COMMUNICATIONS 2023; 3:37. [PMID: 37185952 PMCID: PMC10130141 DOI: 10.1038/s43705-023-00244-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/01/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Metabolite exchange within marine microbial communities transfers carbon and other major elements through global cycles and forms the basis of microbial interactions. Yet lack of gene annotations and concern about the quality of existing ones remain major impediments to revealing currencies of carbon flux. We employed an arrayed mutant library of the marine bacterium Ruegeria pomeroyi DSS-3 to experimentally annotate substrates of organic compound transporter systems, using mutant growth and compound drawdown analyses to link transporters to their cognate substrates. Mutant experiments verified substrates for thirteen R. pomeroyi transporters. Four were previously hypothesized based on gene expression data (taurine, glucose/xylose, isethionate, and cadaverine/putrescine/spermidine); five were previously hypothesized based on homology to experimentally annotated transporters in other bacteria (citrate, glycerol, N-acetylglucosamine, fumarate/malate/succinate, and dimethylsulfoniopropionate); and four had no previous annotations (thymidine, carnitine, cysteate, and 3-hydroxybutyrate). These bring the total number of experimentally-verified organic carbon influx transporters to 18 of 126 in the R. pomeroyi genome. In a longitudinal study of a coastal phytoplankton bloom, expression patterns of the experimentally annotated transporters linked them to different stages of the bloom, and also led to the hypothesis that citrate and 3-hydroxybutyrate were among the most highly available bacterial substrates. Improved functional annotation of the gatekeepers of organic carbon uptake is critical for deciphering carbon flux and fate in microbial ecosystems.
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Affiliation(s)
- William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Hannah E Kepner
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Mario Uchimiya
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Catalina Mejia
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | | | - Christopher R Reisch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA.
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Li C, Jia Z, Zhang S, Li T, Ma S, Cheng X, Chen M, Nie H, Zhai L, Zhang B, Liu X, Zhang J, Müller C. The positive effects of mineral-solubilizing microbial inoculants on asymbiotic nitrogen fixation of abandoned mine soils are driven by keystone phylotype. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163663. [PMID: 37094687 DOI: 10.1016/j.scitotenv.2023.163663] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/03/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Toward the restoration of the increasing numbers of abandoned mines across China, external-soil spray seeding technologies have become more extensively utilized. However, considerable challenges remain that seriously hamper the effectiveness of these technologies, such as inadequate nutrient availability for plants. Previous studies have shown that mineral-solubilizing microbial inoculants can increase the nodules of legumes. However, their effects on symbiotic nitrogen fixation (SNF), asymbiotic nitrogen fixation (ANF), and diazotrophic communities remain unknown. Further, research into the application of functional microorganisms for the restoration of abandoned mines has been conducted either in greenhouses, or their application in the field has been too brief. Thus, we established a four-year field experiment in an abandoned mine and quantified the SNF, ANF, and diazotrophic communities. To the best of our knowledge, this study is the first to describe the long-term application of specific functional microorganisms for the remediation of abandoned mine sites in the field. We revealed that mineral-solubilizing microbial inoculants significantly increased the soil ANF rate and SNF content. There was no significant correlation between the diazotrophic alpha diversity and soil ANF rate; however, there were strong positive associations between the relative abundance and biodiversity of keystone phylotype (module #5) within ecological clusters and the ANF rate. Molecular ecological networks indicated that microbial inoculants increased network complexity and stability. Moreover, the inoculants significantly enhanced the deterministic ratio of diazotrophic communities. Furthermore, homogeneous selection predominantly mediated the assembly of soil diazotrophic communities. It was concluded that mineral-solubilizing microorganisms played a critical role in maintaining and enhancing nitrogen, which offers a new solution with great potential for the restoration of ecosystems at abandoned mine sites.
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Affiliation(s)
- Chong Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China; Institute of Plant Ecology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany.
| | - Zhaohui Jia
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Shuifeng Zhang
- Faculty of Information Technology, Nanjing Forest Police College, Nanjing 210000, China.
| | - Tao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Shilin Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Xuefei Cheng
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Meiling Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Hui Nie
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Lu Zhai
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK 74078, USA; Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Bo Zhang
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Xin Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu 210037, China.
| | - Christoph Müller
- Institute of Plant Ecology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin, Ireland; Liebig Centre for Agroecology and Climate Impact Research, Justus Liebig University, Germany.
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66
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Silverstein MR, Segrè D, Bhatnagar JM. Environmental microbiome engineering for the mitigation of climate change. GLOBAL CHANGE BIOLOGY 2023; 29:2050-2066. [PMID: 36661406 DOI: 10.1111/gcb.16609] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/15/2022] [Indexed: 05/28/2023]
Abstract
Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune activities that regulate the long-term stabilization of carbon in ecosystems. In this review, we outline the process of environmental engineering and synthesize key considerations about ecosystem functions to target, means of sourcing microorganisms, strategies for designing microbial inocula, methods to deliver inocula, and the factors that enable inocula to establish within a resident community and modify an ecosystem function target. Recent work, enabled by high-throughput technologies and modeling approaches, indicate that microbial inocula designed from the top-down, particularly through directed evolution, may generally have a higher chance of establishing within existing microbial communities than other historical approaches to microbiome engineering. We address outstanding questions about the determinants of inocula establishment and provide suggestions for further research about the possibilities and challenges of environmental microbiome engineering as a tool to combat climate change.
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Affiliation(s)
- Michael R Silverstein
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Department of Physics, Boston University, Boston, Massachusetts, USA
| | - Jennifer M Bhatnagar
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
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67
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Cai P, Xiong J, Sha H, Dai X, Lu J. Tumor bacterial markers diagnose the initiation and four stages of colorectal cancer. Front Cell Infect Microbiol 2023; 13:1123544. [PMID: 36992683 PMCID: PMC10040638 DOI: 10.3389/fcimb.2023.1123544] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
Increasing evidence has supported dysbiosis in the faecal microbiome along control-adenoma-carcinoma sequence. In contrast, the data is lacking for in situ tumor bacterial community over colorectal cancer (CRC) progression, resulting in the uncertainties of identifying CRC-associated taxa and diagnosing the sequential CRC stages. Through comprehensive collection of benign polyps (BP, N = 45) and the tumors (N = 50) over the four CRC stages, we explored the dynamics of bacterial communities over CRC progression using amplicons sequencing. Canceration was the primarily factor governing the bacterial community, followed by the CRC stages. Besides confirming known CRC-associated taxa using differential abundance, we identified new CRC driver species based on their keystone features in NetShift, including Porphyromonas endodontalis, Ruminococcus torques and Odoribacter splanchnicus. Tumor environments were less selective for stable core community, resulting in heterogeneity in bacterial communities over CRC progression, as supported by higher average variation degree, lower occupancy and specificity compared with BP. Intriguingly, tumors could recruit beneficial taxa antagonizing CRC-associated pathogens at CRC initiation, a pattern known as “cry-for-help”. By distinguishing age- from CRC stage-associated taxa, the top 15 CRC stage-discriminatory taxa contributed an overall 87.4% accuracy in diagnosing BP and each CRC stage, in which no CRC patients were falsely diagnosed as BP. The accuracy of diagnosis model was unbiased by human age and gender. Collectively, our findings provide new CRC-associated taxa and updated interpretations for CRC carcinogenesis from an ecological perspective. Moving beyond stratifying case-control, the CRC-stage discriminatory taxa could add the diagnosis of BP and the four CRC stages, especially the patients with poor pathological feature and un-reproducibility between two observers.
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Affiliation(s)
- Ping Cai
- Ningbo Second Hospital, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Haonan Sha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Xiaoyu Dai
- Ningbo Second Hospital, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- *Correspondence: Xiaoyu Dai, ; Jiaqi Lu,
| | - Jiaqi Lu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China
- Zhejiang KinGene Bio-technology Co., Ltd, Ningbo, China
- *Correspondence: Xiaoyu Dai, ; Jiaqi Lu,
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Poppeliers SW, Sánchez-Gil JJ, de Jonge R. Microbes to support plant health: understanding bioinoculant success in complex conditions. Curr Opin Microbiol 2023; 73:102286. [PMID: 36878082 DOI: 10.1016/j.mib.2023.102286] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/24/2023] [Accepted: 02/02/2023] [Indexed: 03/07/2023]
Abstract
A promising, sustainable way to enhance plant health and productivity is by leveraging beneficial microbes. Beneficial microbes are natural soil residents with proven benefits for plant performance and health. When applied in agriculture to improve crop yield and performance, these microbes are commonly referred to as bioinoculants. Yet, despite their promising properties, bioinoculant efficacy can vary dramatically in the field, hampering their applicability. Invasion of the rhizosphere microbiome is a critical determinant for bioinoculant success. Invasion is a complex phenomenon that is shaped by interactions with the local, resident microbiome and the host plant. Here, we explore all of these dimensions by cross-cutting ecological theory and molecular biology of microbial invasion in the rhizosphere. We refer to the famous Chinese philosopher and strategist Sun Tzu, who believed that solutions for problems require deep understanding of the problems themselves, to review the major biotic factors determining bioinoculant effectiveness.
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Affiliation(s)
- Sanne Wm Poppeliers
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Juan J Sánchez-Gil
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
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Li H, Luo QP, Zhao S, Zhou YY, Huang FY, Yang XR, Su JQ. Effect of phenol formaldehyde-associated microplastics on soil microbial community, assembly, and functioning. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130288. [PMID: 36335899 DOI: 10.1016/j.jhazmat.2022.130288] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Increasing investigations explore the effects of plastic pollutants on bacterial communities, diversity, and functioning in various ecosystems. However, the impact of microplastics (MPs) on the eukaryotic community, microbial assemblages, and interactions is still limited. Here, we investigated bacterial and micro-eukaryotic communities and functioning in soils with different concentrations of phenol formaldehyde-associated MPs (PF-MPs), and revealed the factors, such as soil properties, microbial community assembly, and interactions between microbes, influencing them. Our results showed that a high concentration (1%) of PF-MPs decreased the microbial interactions and the contribution of deterministic processes to the community assembly of microbes, and consequently changed the communities of bacteria, but not eukaryotes. A significant and negative relationship was determined between N2O emission rate and functional genes related to nitrification, indicating that the competitive interactions between functional microbes would affect the nitrogen cycling of soil ecosystem. We further found that vegetable biomass weakly decreased in treatments with a higher concentration of PF-MPs and positively related to the diversity of micro-eukaryotic communities and functional diversity of bacterial communities. These results suggest that a high concentration of the PF-MPs would influence crop growth by changing microbial communities, interactions, and eukaryotic and functional diversity. Our findings provide important evidence for agriculture management of phenol formaldehyde and suggest that we must consider their threats to microbial community compositions, diversity, and assemblage in soils due to the accumulation of PF-MPs widely used in the field.
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Affiliation(s)
- Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, PR China.
| | - Qiu-Ping Luo
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Sha Zhao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Yan-Yan Zhou
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Fu-Yi Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, PR China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, PR China.
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70
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Karlsson ME, Hellström M, Flöhr A, Bergstrand KJ, Alsanius BW. The power of light: Impact on the performance of biocontrol agents under minimal nutrient conditions. Front Microbiol 2023; 14:1087639. [PMID: 36819051 PMCID: PMC9932321 DOI: 10.3389/fmicb.2023.1087639] [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: 11/02/2022] [Accepted: 01/17/2023] [Indexed: 02/05/2023] Open
Abstract
Background The spectral distribution of light (different wavelength) has recently been identified as an important factor in the dynamics and function of leaf-associated microbes. This study investigated the impact of different wavelength on three commercial biocontrol agents (BCA): Bacillus amyloliquefaciens (BA), Pseudomonas chlororaphis (PC), and Streptomyces griseoviridis (SG). Methods The impact of light exposure on sole carbon source utilization, biofilm formation, and biosurfactant production by the selected BCA was studied using phenotypic microarray (PM) including 190 sole carbon sources (OmniLog®, PM panels 1 and 2). The BCA were exposed to five monochromatic light conditions (420, 460, 530, 630, and 660 nm) and darkness during incubation, at an intensity of 50 μmol m-2 s-1. Results Light exposure together with specific carbon source increased respiration in all three BCA. Different wavelengths of light influenced sole carbon utilization for the different BCA, with BA and PC showing increased respiration when exposed to wavelengths within the blue spectrum (420 and 460 nm) while respiration of selected carbon sources by SG increased in the presence of red light (630 and 660 nm). Only one carbon source (capric acid) generated biosurfactant production in all three BCA. A combination of specific wavelength of light and sole carbon source increased biofilm formation in all three BCA. BA showed significantly higher biofilm formation when exposed to blue (460 nm) and green (530 nm) light and propagated in D-sucrose, D-fructose, and dulcitol. PC showed higher biofilm formation when exposed to blue light. Biofilm formation by SG increased when exposed to red light (630 nm) and propagated in citraconic acid. Conclusion To increase attachment and success in BCA introduced into the phyllosphere, a suitable combination of light quality and nutrient conditions could be used.
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Dai W, Ye J, Xue Q, Liu S, Xu H, Liu M, Lin Z. Changes in Bacterial Communities of Kumamoto Oyster Larvae During Their Early Development and Following Vibrio Infection Resulting in a Mass Mortality Event. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:30-44. [PMID: 36370246 DOI: 10.1007/s10126-022-10178-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Vibrio and Ostreid herpesvirus 1 are responsible for mass mortalities of oyster larvae in hatcheries. Relevant works have focused on their relationships with the disease when larval mortality occurs. On the contrary, little is known about how the resident microbiota in oyster larvae responds to Vibrio-infected disease causing mortality as the disease progressed, whereas this knowledge is fundamental to unveil the etiology of the disease. Here, we analyzed the temporal succession of the microbiome of Kumamoto oyster (Crassostrea sikamea) larvae during their early development, accompanied by a Vibrio-caused mortality event that occurred at the post D-stage of larval development in a shellfish hatchery in Ningbo, China, on June 2020. The main causative agent of larval mortality was attributable to Vibrio infection, which was confirmed by linearly increased Vibrio abundance over disease progression. Larval bacterial communities dramatically changed over host development and disease progression, as highlighted by reduced α-diversity and less diverse core taxa when the disease occurred. Null model and phylogenetic-based mean nearest taxon distance analyses showed that the relative importance of deterministic processes governing larval bacterial assembly initially increased over host development, whereas this dominance was depleted over disease progression. Furthermore, we screened the disease-discriminatory taxa with a significant change in their relative abundances, which could be indicative of disease progression. In addition, network analysis revealed that disease occurrence remodeled the co-occurrence patterns and niche characteristics of larval microbiota. Our findings demonstrate that the dysbiosis of resident bacterial communities and the shift of microecological mechanisms in the larval microbiome may contribute to mortality during oyster early development.
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Affiliation(s)
- Wenfang Dai
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Jing Ye
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Qinggang Xue
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China.
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China.
| | - Sheng Liu
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Hongqiang Xu
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Minhai Liu
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Zhihua Lin
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China.
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China.
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72
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Morales Moreira ZP, Chen MY, Yanez Ortuno DL, Haney CH. Engineering plant microbiomes by integrating eco-evolutionary principles into current strategies. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102316. [PMID: 36442442 DOI: 10.1016/j.pbi.2022.102316] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Engineering plant microbiomes has the potential to improve plant health in a rapid and sustainable way. Rapidly changing climates and relatively long timelines for plant breeding make microbiome engineering an appealing approach to improving food security. However, approaches that have shown promise in the lab have not resulted in wide-scale implementation in the field. Here, we suggest the use of an integrated approach, combining mechanistic molecular and genetic knowledge, with ecological and evolutionary theory, to target knowledge gaps in plant microbiome engineering that may facilitate translatability of approaches into the field. We highlight examples where understanding microbial community ecology is essential for a holistic understanding of the efficacy and consequences of microbiome engineering. We also review examples where understanding plant-microbe evolution could facilitate the design of plants able to recruit specific microbial communities. Finally, we discuss possible trade-offs in plant-microbiome interactions that should be considered during microbiome engineering efforts so as not to introduce off-target negative effects. We include classic and emergent approaches, ranging from microbial inoculants to plant breeding to host-driven microbiome engineering, and address areas that would benefit from multidisciplinary approaches.
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Affiliation(s)
- Zayda P Morales Moreira
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Melissa Y Chen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Daniela L Yanez Ortuno
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Cara H Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
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73
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Barron AJ, Lesperance DNA, Doucette J, Calle S, Broderick NA. Microbiome derived acidity protects against microbial invasion in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523836. [PMID: 36711873 PMCID: PMC9882140 DOI: 10.1101/2023.01.12.523836] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microbial invasions underlie host-microbe interactions that result in microbial pathogenesis and probiotic colonization. While these processes are of broad interest, there are still gaps in our understanding of the barriers to entry and how some microbes overcome them. In this study, we explore the effects of the microbiome on invasions of foreign microbes in Drosophila melanogaster. We demonstrate that gut microbes Lactiplantibacillus plantarum and Acetobacter tropicalis improve survival during invasion of a lethal gut pathogen and lead to a reduction in microbial burden. Using a novel multi-organism interactions assay, we report that L. plantarum inhibits the growth of three invasive Gram-negative bacteria, while A. tropicalis prevents this inhibition. A series of in vitro and in vivo experiments revealed that inhibition by L. plantarum is linked to its ability to acidify both internal and external environments, including culture media, fly food, and the gut itself, while A. tropicalis diminishes the inhibition by quenching acids. We propose that acid produced by the microbiome serves as an important gatekeeper to microbial invasions, as only microbes capable of tolerating acidic environments can colonize the host. The methods described herein will add to the growing breadth of tools to study microbe-microbe interactions in broad contexts.
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Affiliation(s)
- Alexander J. Barron
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218 U.S.A
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 U.S.A
| | - Danielle N. A. Lesperance
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218 U.S.A
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 U.S.A
| | - Jeremy Doucette
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 U.S.A
| | - Sthefany Calle
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 U.S.A
| | - Nichole A. Broderick
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218 U.S.A
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 U.S.A
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74
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Osińska A, Korzeniewska E, Korzeniowska-Kowal A, Wzorek A, Harnisz M, Jachimowicz P, Buta-Hubeny M, Zieliński W. The challenges in the identification of Escherichia coli from environmental samples and their genetic characterization. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:11572-11583. [PMID: 36094711 PMCID: PMC9898413 DOI: 10.1007/s11356-022-22870-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Escherichia coli bacteria are an essential indicator in evaluations of environmental pollution, which is why they must be correctly identified. This study aimed to determine the applicability of various methods for identifying E. coli strains in environmental samples. Bacterial strains preliminary selected on mFc and Chromocult media as E. coli were identified using MALDI Biotyper techniques, based on the presence of genes characteristic of E. coli (uidA, uspA, yaiO), as well as by 16S rRNA gene sequencing. The virulence and antibiotic resistance genes pattern of bacterial strains were also analyzed to investigate the prevalence of factors that may indicate adaptation to unsupportive environmental conditions and could have any significance in further identification of E. coli. Of the strains that had been initially identified as E. coli with culture-based methods, 36-81% were classified as E. coli with the use of selected techniques. The value of Cohen's kappa revealed the highest degree of agreement between the results of 16S rRNA gene sequencing, the results obtained in the MALDI Biotyper system, and the results of the analysis based on the presence of the yaiO gene. The results of this study could help in the selection of more accurate and reliable methods which can be used in a preliminary screening and more precise identification of E. coli isolated from environmental samples.
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Affiliation(s)
- Adriana Osińska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland.
| | - Agnieszka Korzeniowska-Kowal
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114, Wroclaw, Poland
| | - Anna Wzorek
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114, Wroclaw, Poland
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Piotr Jachimowicz
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Martyna Buta-Hubeny
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
| | - Wiktor Zieliński
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720, Olsztyn, Poland
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75
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McMullen JG, Lennon JT. Mark-recapture of microorganisms. Environ Microbiol 2023; 25:150-157. [PMID: 36310117 DOI: 10.1111/1462-2920.16267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 01/21/2023]
Affiliation(s)
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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76
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Zhang Y, Yang Y, Yu L, Wang A, Xue C, Zhang J, Duan A, Zhao M. Composition and characteristics of soil microbial communities in cotton fields with different incidences of Verticillium wilt. PLANT SIGNALING & BEHAVIOR 2022; 17:2034271. [PMID: 35175867 PMCID: PMC9746606 DOI: 10.1080/15592324.2022.2034271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 06/13/2023]
Abstract
Soil microorganisms could affect the growth of plants and play an important role in indicating the change of soil environment. Cotton Verticillium wilt is a serious soil borne disease. This study aimed to analyze the community characteristics of soil microorganisms in cotton fields with different incidences of Verticillium wilt, so as to provide theoretical guidance for the prevention and control of soil borne diseases of cotton. Through the analysis of soil microbial communities in six fields, the results showed that there was no difference in fungal and bacterial alpha-diversity index before cotton planting, while there were differences in rhizosphere of diseased plants. For fungal beta diversity indexes, there were significant differences in these six fields. There was no significant difference for bacterial beta diversity indexes before cotton planting, while there was a certain difference in the rhizosphere of diseased cotton plants. The composition of fungi and bacteria in different fields was roughly the same at the genus level, but the abundances of the same genus varied greatly between different fields. Before cotton planting, there were 61 fungi (genera) and 126 bacteria (genera) with different abundances in the six fields. Pseudomonas, Sphingomonas and Burkholderia had higher abundances in the fields with less incidence. This study will provide a theoretical basis for microbial control of Cotton Verticillium wilt.
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Affiliation(s)
- Yun Zhang
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yuanxue Yang
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lang Yu
- Plant Protection Station of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Aiyu Wang
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chao Xue
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jianhua Zhang
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ailing Duan
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ming Zhao
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
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77
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Impact of Plant-Beneficial Bacterial Inocula on the Resident Bacteriome: Current Knowledge and Future Perspectives. Microorganisms 2022; 10:microorganisms10122462. [PMID: 36557714 PMCID: PMC9781654 DOI: 10.3390/microorganisms10122462] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
The inoculation of plant growth-promoting bacteria (PGPB) as biofertilizers is one of the most efficient and sustainable strategies of rhizosphere manipulation leading to increased plant biomass and yield and improved plant health, as well as the ameliorated nutritional value of fruits and edible seeds. During the last decades, exciting, but heterogeneous, results have been obtained growing PGPB inoculated plants under controlled, stressful, and open field conditions. On the other hand, the possible impact of the PGPB deliberate release on the resident microbiota has been less explored and the little available information is contradictory. This review aims at filling this gap: after a brief description of the main mechanisms used by PGPB, we focus our attention on the process of PGPB selection and formulation and we provide some information on the EU regulation for microbial inocula. Then, the concept of PGPB inocula as a tool for rhizosphere engineering is introduced and the possible impact of bacterial inoculant on native bacterial communities is discussed, focusing on those bacterial species that are included in the EU regulation and on other promising bacterial species that are not yet included in the EU regulation.
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78
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Piccardi P, Alberti G, Alexander JM, Mitri S. Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves. THE ISME JOURNAL 2022; 16:2644-2652. [PMID: 36104451 PMCID: PMC9666444 DOI: 10.1038/s41396-022-01314-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/27/2022] [Accepted: 08/24/2022] [Indexed: 12/15/2022]
Abstract
Predicting whether microbial invaders will colonize an environment is critical for managing natural and engineered ecosystems, and controlling infectious disease. Invaders often face competition by resident microbes. But how invasions play out in communities dominated by facilitative interactions is less clear. We previously showed that growth medium toxicity can promote facilitation between four bacterial species, as species that cannot grow alone rely on others to survive. Following the same logic, here we allowed other bacterial species to invade the four-species community and found that invaders could more easily colonize a toxic medium when the community was present. In a more benign environment instead, invasive species that could survive alone colonized more successfully when the residents were absent. Next, we asked whether early colonists could exclude future ones through a priority effect, by inoculating the invaders into the resident community only after its members had co-evolved for 44 weeks. Compared to the ancestral community, the co-evolved resident community was more competitive toward invaders and less affected by them. Our experiments show how communities may assemble by facilitating one another in harsh, sterile environments, but that arriving after community members have co-evolved can limit invasion success.
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Affiliation(s)
- Philippe Piccardi
- Département de Microbiologie Fondamentale, Université de Lausanne, Lausanne, Switzerland
| | - Géraldine Alberti
- Département de Microbiologie Fondamentale, Université de Lausanne, Lausanne, Switzerland
| | - Jake M Alexander
- Department of Environmental Systems Science, ETH Zurich, Zürich, Switzerland
| | - Sara Mitri
- Département de Microbiologie Fondamentale, Université de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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79
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Nguyen UT, Kalan LR. Forgotten fungi: the importance of the skin mycobiome. Curr Opin Microbiol 2022; 70:102235. [PMID: 36372041 PMCID: PMC10044452 DOI: 10.1016/j.mib.2022.102235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/21/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022]
Abstract
The mosaic ecosystems of microbes that live on our skin encompass not only bacteria but also fungi, microeukaryotes, and viruses. As the second most prevalent group, unique fungal communities are found across the dry, moist, and oily microenvironments of human skin, and alterations of these communities are largely driven by changes in skin physiology throughout an individual's lifespan. Fungi have also been associated with infection and dermatological disorders, resulting from the disrupted balance between fungal-bacterial networks on the skin. Mechanisms of colonization resistance toward fungi in the skin microbiome of animals have advanced our understanding in conservation strategies, yet in the human skin, the fungal microbiome (mycobiome) remains vastly unexplored. Here, we review recent studies on the role of fungi in the skin microbiome, emphasizing how fungal-bacterial interactions at the skin surface play an important ecological function in vertebrate hosts.
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Affiliation(s)
- Uyen Thy Nguyen
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States; Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States.
| | - Lindsay R Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States; Department of Medicine, Division of Infectious Disease, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States.
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80
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Kim DY, Jeong IC, Lee SY, Jeong YS, Han JE, Tak EJ, Lee JY, Kim PS, Hyun DW, Bae JW. Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748471 DOI: 10.1099/ijsem.0.005643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Two novel Gram-stain-positive, non-motile and non-spore-forming bacterial strains, designated J2M5T and J1M15T, were isolated from the gastrointestinal tract of a lake prawn Palaemon paucidens. Strain J2M5T was an obligately aerobic bacterium that formed milky-coloured colonies and showed a rod-coccus cell cycle, while strain J1M15T was a facultatively aerobic bacterium that formed orangish-yellow-coloured colonies and showed rod-shaped cells. Strains J2M5T and J1M15T showed the highest 16S rRNA gene sequence similarity to Nocardioides ganghwensis JC2055T (98.63 %) and Tessaracoccus flavescens SST-39T (98.08 %), respectively. The whole-genome sequence of strain J2M5T was 4.52 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J2M5T was 72.5 mol%. The whole-genome sequence of strain J1M15T was 3.20 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J1M15T was 69.6mol %. Strains J2M5T and J1M15T showed high OrthoANI similarity to N. ganghwensis JC2055T (83.6 %) and T. flavescens (77.2 %), respectively. We analysed the genome sequences of strains J2M5T and J1M15T in terms of carbohydrate-active enzymes, antibiotic resistance genes and virulence factor genes. Strains J2M5T and J1M15T contained MK-8 (H4) and MK-9 (H4) as the predominant respiratory quinones, respectively. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Additionally, strain J2M5T possessed phosphatidylcholine, phosphatidylserine and phosphatidylethanolamine. The cellular sugar components of strain J2M5T were ribose, mannose, glucose and galactose, and its cellular amino acid components were l-alanine and l-lysine. The cellular sugar components of strain J1M15T were rhamnose, ribose, mannose and glucose, and its cellular amino acid component was l-alanine. The major cellular fatty acids of strains J2M5T and J1M15T were iso-C16 : 0 and anteiso-C15 : 0, respectively. The multiple taxonomic analyses indicated that strains J2M5T and J1M15T represent novel species of the genus Nocardioides and Tessaracoccus, respectively. We propose the names Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov. for strain J2M5T (=KCTC 49461T=CCUG 74767T) and strain J1M15T (=KCTC 49462T=CCUG 74766T), respectively.
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Affiliation(s)
- Do-Yeon Kim
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - In-Chul Jeong
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - So-Yeon Lee
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yun-Seok Jeong
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jeong Eun Han
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Euon Jung Tak
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - June-Young Lee
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea.,Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
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81
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Wang J, Lang H, Zhang W, Zhai Y, Zheng L, Chen H, Liu Y, Zheng H. Stably transmitted defined microbial community in honeybees preserves Hafnia alvei inhibition by regulating the immune system. Front Microbiol 2022; 13:1074153. [PMID: 36532452 PMCID: PMC9751035 DOI: 10.3389/fmicb.2022.1074153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/14/2022] [Indexed: 12/08/2023] Open
Abstract
The gut microbiota of honeybees is highly diverse at the strain level and essential to the proper function and development of the host. Interactions between the host and its gut microbiota, such as specific microbes regulating the innate immune system, protect the host against pathogen infections. However, little is known about the capacity of these strains deposited in one colony to inhibit pathogens. In this study, we assembled a defined microbial community based on phylogeny analysis, the 'Core-20' community, consisting of 20 strains isolated from the honeybee intestine. The Core-20 community could trigger the upregulation of immune gene expressions and reduce Hafnia alvei prevalence, indicating immune priming underlies the microbial protective effect. Functions related to carbohydrate utilization and the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS systems) are represented in genomic analysis of the defined community, which might be involved in manipulating immune responses. Additionally, we found that the defined Core-20 community is able to colonize the honeybee gut stably through passages. In conclusion, our findings highlight that the synthetic gut microbiota could offer protection by regulating the host immune system, suggesting that the strain collection can yield insights into host-microbiota interactions and provide solutions to protect honeybees from pathogen infections.
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Affiliation(s)
- Jieni Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Haoyu Lang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Wenhao Zhang
- Faculty of Agriculture and Food, Kunming University of Science and Technology, Kunming, China
| | - Yifan Zhai
- Shandong Academy of Agricultural Sciences, Institute of Plant Protection, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Li Zheng
- Shandong Academy of Agricultural Sciences, Institute of Plant Protection, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Hao Chen
- Shandong Academy of Agricultural Sciences, Institute of Plant Protection, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Yan Liu
- Shandong Academy of Agricultural Sciences, Institute of Plant Protection, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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82
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Park S, Jung D, Altshuler I, Kurban D, Dufour S, Ronholm J. A longitudinal census of the bacterial community in raw milk correlated with Staphylococcus aureus clinical mastitis infections in dairy cattle. Anim Microbiome 2022; 4:59. [PMID: 36434660 PMCID: PMC9701008 DOI: 10.1186/s42523-022-00211-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is a common cause of clinical mastitis (CM) in dairy cattle. Optimizing the bovine mammary gland microbiota to resist S. aureus colonization is a growing area of research. However, the details of the interbacterial interactions between S. aureus and commensal bacteria, which would be required to manipulate the microbiome to resist infection, are still unknown. This study aims to characterize changes in the bovine milk bacterial community before, during, and after S. aureus CM and to compare bacterial communities present in milk between infected and healthy quarters. METHODS We collected quarter-level milk samples from 698 Holstein dairy cows over an entire lactation. A total of 11 quarters from 10 cows were affected by S. aureus CM and milk samples from these 10 cows (n = 583) regardless of health status were analyzed by performing 16S rRNA gene amplicon sequencing. RESULTS The milk microbiota of healthy quarters was distinguishable from that of S. aureus CM quarters two weeks before CM diagnosis via visual inspection. Microbial network analysis showed that 11 OTUs had negative associations with OTU0001 (Staphylococcus). A low diversity or dysbiotic milk microbiome did not necessarily correlate with increased inflammation. Specifically, Staphylococcus xylosus, Staphylococcus epidermidis, and Aerococcus urinaeequi were each abundant in milk from the quarters with low levels of inflammation. CONCLUSION Our results show that the udder microbiome is highly dynamic, yet a change in the abundance in certain bacteria can be a potential indicator of future S. aureus CM. This study has identified potential prophylactic bacterial species that could act as a barrier against S. aureus colonization and prevent future instances of S. aureus CM.
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Affiliation(s)
- Soyoun Park
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, QC, Canada
- Mastitis Network, Saint-Hyacinthe, QC, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, QC, Canada
| | - Dongyun Jung
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, QC, Canada
- Mastitis Network, Saint-Hyacinthe, QC, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, QC, Canada
| | - Ianina Altshuler
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, QC, Canada
| | - Daryna Kurban
- Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Mastitis Network, Saint-Hyacinthe, QC, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, QC, Canada
| | - Simon Dufour
- Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
- Mastitis Network, Saint-Hyacinthe, QC, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, QC, Canada
| | - Jennifer Ronholm
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, QC, Canada.
- Mastitis Network, Saint-Hyacinthe, QC, Canada.
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, QC, Canada.
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Henriksen NNSE, Schostag MD, Balder SR, Bech PK, Strube ML, Sonnenschein EC, Gram L. The ability of Phaeobacter inhibens to produce tropodithietic acid influences the community dynamics of a microalgal microbiome. ISME COMMUNICATIONS 2022; 2:109. [PMID: 37938341 PMCID: PMC9723703 DOI: 10.1038/s43705-022-00193-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2023]
Abstract
Microbial secondary metabolites facilitate microbial interactions and are crucial for understanding the complexity of microbial community dynamics. The purpose of the present study was to determine how a secondary metabolite producing marine bacteria or its metabolite deficient mutant affected the microbiome of the marine microalgae Tetraselmis suecica during a 70 day long co-evolution experiment. Using 16S rRNA gene amplicon sequencing, we found that neither the tropodithietic acid (TDA)-producing Phaeobacter inhibens wildtype nor the TDA-deficient mutant had major impacts on the community composition. However, a subset of strains, displayed temporally different relative abundance trajectories depending on the presence of P. inhibens. In particular, a Winogradskyella strain displayed temporal higher relative abundance when the TDA-producing wildtype was present. Numbers of the TDA-producing wildtype were reduced significantly more than those of the mutant over time indicating that TDA production was not an advantage. In communities without the P. inhibens wildtype strain, an indigenous population of Phaeobacter increased over time, indicating that indigenous Phaeobacter populations cannot co-exist with the TDA-producing wildtype. Despite that TDA was not detected chemically, we detected transcripts of the tdaC gene indicating that TDA could be produced in the microbial community associated with the algae. Our work highlights the importance of deciphering longitudinal strain dynamics when addressing the ecological effect of secondary metabolites in a relevant natural community.
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Affiliation(s)
| | - Morten Dencker Schostag
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
| | - Simone Rosen Balder
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
| | - Pernille Kjersgaard Bech
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
| | - Eva Christina Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark
- Department of Biosciences, Swansea University, Singleton Park, SA2 8PP, Swansea, United Kingdom
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Bldg. 221, DK-2800 Kgs, Lyngby, Denmark.
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84
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Li W, Wang Z, He S. Effects of species richness and nutrient availability on the invasibility of experimental microalgal microcosms. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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85
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Xing J, Chen M, Deng X, Chen J, Jiang P, Qin H. Resilience of soil microbial metabolic functions to temporary E. coli invasion. CHEMOSPHERE 2022; 307:135906. [PMID: 35944672 DOI: 10.1016/j.chemosphere.2022.135906] [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: 06/12/2022] [Revised: 07/23/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Due to the globalization and increasing human activities, there is a significant increase in bacterial invasions to the soil ecosystems. Soil resident communities are vulnerable to bacterial invasion and suffered legacy effects after unsuccessful invasion. However, whether such changes in the soil ecosystems are permanent or temporary remains unclear. Here, we investigated the functional resilience of soil ecosystems to bacterial invasion and intensive managements. We used Escherichia coli O157:H7 (E. coli) as model strain examined the soil microbial metabolic functions, including enzyme activities, nitrogen and carbon use efficiency, community niche, and carbon metabolic potential, as well as soil physicochemical properties and microbial invader survival in 8 soil samples, 4 from natural hardwood forests and 4 from intensively managed Moso bamboo forests. The results showed that soil ecosystems were not resistant to E. coli invasion regardless of the intensity of management, which the finding was significantly reflected in the nutrient-acquiring activities or carbon utilization, or both. Besides, the invasion legacy effect (the effect after invader apoptosis) was positively related to E. coli survival time. However, most of the metabolic functions could recover almost to the initial state after 135 days of incubation, suggesting a strong recovery capacity of the soil ecosystems. These data indicate that E. coli invasion has a legacy effect on the functions of soil resident communities. However, soil ecosystems are highly resilient even under intensive human management.
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Affiliation(s)
- Jiajia Xing
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Min Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junhui Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Peikun Jiang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Hua Qin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, 311300, China.
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86
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Klimasmith IM, Kent AD. Micromanaging the nitrogen cycle in agroecosystems. Trends Microbiol 2022; 30:1045-1055. [PMID: 35618540 DOI: 10.1016/j.tim.2022.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/29/2022] [Accepted: 04/29/2022] [Indexed: 01/13/2023]
Abstract
While large inputs of synthetic nitrogen fertilizers enable our current rate of crop production and feed a growing global population, these fertilizers come at a heavy environmental cost. Driven by microbial processes, excess applied nitrogen is lost from agroecosystems as nitrate and nitrous oxide (N2O) contaminating aquatic ecosystems and contributing to climate change. Interest in nitrogen-fixing microorganisms as an alternative to synthetic fertilizers is rapidly accelerating. Microbial inoculants offer the promise of a sustainable and affordable source of nitrogen, but the impact of inoculants on nitrogen dynamics at an ecosystem level is not fully understood. This review synthesizes recent studies on microbial inoculants as tools for nutrient management and considers the ramifications of inoculants for nitrogen transformations beyond fixation.
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Affiliation(s)
- Isaac M Klimasmith
- Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Angela D Kent
- Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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87
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Phenomenology and dynamics of competitive ecosystems beyond the niche-neutral regimes. Proc Natl Acad Sci U S A 2022; 119:e2204394119. [PMID: 36251996 PMCID: PMC9618050 DOI: 10.1073/pnas.2204394119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Structure, composition, and stability of ecological populations are shaped by the inter- and intraspecies interactions within their communities. It remains to be fully understood how the interplay of these interactions with other factors, such as immigration, controls the structure, the diversity, and the long-term stability of ecological systems in the presence of noise and fluctuations. We address this problem using a minimal model of interacting multispecies ecological communities that incorporates competition, immigration, and demographic noise. We find that a complete phase diagram exhibits rich behavior with multiple regimes that go beyond the classical "niche" and "neutral" regimes, extending and modifying the "rare biosphere" or "niche-like" dichotomy. In particular, we observe regimes that cannot be characterized as either niche or neutral where a multimodal species abundance distribution is observed. We characterize the transitions between the different regimes and show how these arise from the underlying kinetics of the species turnover, extinction, and invasion. Our model serves as a minimal null model of noisy competitive ecological systems, against which more complex models that include factors such as mutations and environmental noise can be compared.
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88
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Lu Q, Hu C, Cai L, Wu C, Zhang H, Wei L, Zhang T, Hu H, Liu S, Lei J, Ge T, Dai L, Yang J, Chen J. Changes in soil fungal communities after onset of wheat yellow mosaic virus disease. Front Bioeng Biotechnol 2022; 10:1033991. [PMID: 36324899 PMCID: PMC9621598 DOI: 10.3389/fbioe.2022.1033991] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/30/2022] [Indexed: 10/29/2023] Open
Abstract
Rhizosphere-associated microbes have important implications for plant health, but knowledge of the association between the pathological conditions of soil-borne virus-infected wheat and soil microbial communities, especially changes in fungal communities, remains limited. We investigated the succession of fungal communities from bulk soil to wheat rhizosphere soil in both infected and healthy plants using amplicon sequencing methods, and assessed their potential role in plant health. The results showed that the diversity of fungi in wheat rhizosphere and bulk soils significantly differed post wheat yellow mosaic virus disease onset. The structure differences in fungal community at the two wheat health states or two compartment niches were evident, soil physicochemical properties (i.e., NH4 +) contribute to differences in fungal community structure and alpha diversity. Comparison analysis showed Mortierellomycetes and Dothideomycetes as dominant communities in healthy wheat soils at class level. The genus Pyronemataceae and Solicoccozyma were significantly are significantly enriched in rhizosphere soil of diseased plant, the genus Cystofilobasidium, Cladosporium, Mortierella, and Stephanonectria are significantly enriched in bulk soil of healthy plant. Co-occurrence network analysis showed that the fungi in healthy wheat soil has higher mutual benefit and connectivity compared with diseased wheat. The results of this study demonstrated that the occurrence of wheat yellow mosaic virus diseases altered both fungal community diversity and composition, and that NH4 + is the most important soil physicochemical factor influencing fungal diversity and community composition.
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Affiliation(s)
- Qisen Lu
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Cailin Hu
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Linna Cai
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Chuanfa Wu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Haoqing Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Liang Wei
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tianye Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Haichao Hu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shuang Liu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jiajia Lei
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tida Ge
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
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89
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Gao Y, Jiang X, Wu H, Tong J, Ren X, Ren J, Wu Q, Ye J, Li C, Shi J. Colonization of Penicillium oxalicum SL2 in Pb-contaminated paddy soil and its immobilization effect on soil Pb. J Environ Sci (China) 2022; 120:53-62. [PMID: 35623772 DOI: 10.1016/j.jes.2021.12.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 06/15/2023]
Abstract
Penicillium oxalicum SL2 (SL2) is a previously screened Pb-tolerant fungus that can promote crops growth. The relationship between SL2 colonization and Pb immobilization was studied to provide a theoretical basis for microbial remediation of Pb-contaminated paddy soil. In this study, green fluorescent protein (GFP) labeled SL2 was inoculated into different Pb-contaminated paddy soils (S1-S6). The Pb extracted from the soil by HNO3, EDTA and CaCl2 were used to characterize the available Pb. The results showed that the colonization of SL2 was divided into lag phase (0-7 days), growth phase (7-30 days), and mortality phase (30-90 days). SL2 colonized well in sandy soils rich in clay and total phosphorus with initial pH of 4.5-7.0. In addition, SL2 increased soil pH and decreased soil Eh, which was beneficial to immobilize Pb. In different soils, the highest percentages of CaCl2-Pb, EDTA-Pb, and HNO3-Pb immobilized by SL2 were 34.34%-40.53%, 17.05%-20.11%, and 7.39%-15.62%, respectively. Pearson correlation analysis showed that the percentages of CaCl2-Pb and EDTA-Pb immobilized by SL2 were significantly positively correlated with the number of SL2 during the growth phase. SL2 mainly immobilized Pb in the growth phase and a higher peak number of SL2 was beneficial to the immobilization of Pb.
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Affiliation(s)
- Yu Gao
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; MOE Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Xiaohan Jiang
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; MOE Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Hanxin Wu
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; MOE Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Jianhao Tong
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; MOE Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Xinyue Ren
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Jiayu Ren
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Qianhua Wu
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; MOE Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Jien Ye
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; MOE Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Chunhui Li
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; MOE Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Jiyan Shi
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; MOE Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China.
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90
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Mawarda PC, Le Roux X, Acosta MU, van Elsas JD, Salles JF. The impact of protozoa addition on the survivability of Bacillus inoculants and soil microbiome dynamics. ISME COMMUNICATIONS 2022; 2:82. [PMID: 37938668 PMCID: PMC9723691 DOI: 10.1038/s43705-022-00166-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 10/06/2023]
Abstract
Protists' selective predation of bacterial cells is an important regulator of soil microbiomes, which might influence the success of bacterial releases in soils. For instance, the survival and activity of introduced bacteria can be affected by selective grazing on resident communities or the inoculant, but this remains poorly understood. Here, we investigated the impact of the introduction in the soil of two protozoa species, Rosculus terrestris ECOP02 and/or Cerocomonas lenta ECOP01, on the survival of the inoculants Bacillus mycoides M2E15 (BM) or B. pumilus ECOB02 (BP). We also evaluated the impact of bacterial inoculation with or without protozoan addition on the abundance and diversity of native soil bacterial and protist communities. While the addition of both protozoa decreased the survival of BM, their presence contrarily increased the BP abundance. Protists' selective predation governs the establishment of these bacterial inoculants via modifying the soil microbiome structure and the total bacterial abundance. In the BP experiment, the presence of the introduced protozoa altered the soil community structures and decreased soil bacterial abundance at the end of the experiment, favouring the invader survival. Meanwhile, the introduced protozoa did not modify the soil community structures in the BM experiment and reduced the BM + Protozoa inoculants' effect on total soil bacterial abundance. Our study reinforces the view that, provided added protozoa do not feed preferentially on bacterial inoculants, their predatory behaviour can be used to steer the soil microbiome to improve the success of bacterial inoculations by reducing resource competition with the resident soil microbial communities.
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Affiliation(s)
- Panji Cahya Mawarda
- Microbial Community Ecology Cluster, Expertise Group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
- Research Center for Environment and Clean Technology, National Research and Innovation Agency Republic of Indonesia (BRIN), Komplek LIPI Bandung, Jalan Sangkuriang Gedung 50, Bandung, 40135, Indonesia.
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne, INRAE, CNRS, Université de Lyon, Université Lyon 1, UMR INRAE 1418, UMR CNRS 5557, 43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne, France
| | - Melissa Uribe Acosta
- Plant-Microbe Interactions Group, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Pollution Diagnostics and Control Group (GDCON), Biology Institute, University Research Campus (SIU), University of Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia
| | - Jan Dirk van Elsas
- Microbial Community Ecology Cluster, Expertise Group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Joana Falcão Salles
- Microbial Community Ecology Cluster, Expertise Group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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91
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Deng X, Zhang N, Li Y, Zhu C, Qu B, Liu H, Li R, Bai Y, Shen Q, Falcao Salles J. Bio-organic soil amendment promotes the suppression of Ralstonia solanacearum by inducing changes in the functionality and composition of rhizosphere bacterial communities. THE NEW PHYTOLOGIST 2022; 235:1558-1574. [PMID: 35569105 DOI: 10.1111/nph.18221] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Stimulating the development of soil suppressiveness against certain pathogens represents a sustainable solution toward reducing pesticide use in agriculture. However, understanding the dynamics of suppressiveness and the mechanisms leading to pathogen control remain largely elusive. Here, we investigated the mechanisms used by the rhizosphere microbiome induces bacterial wilt disease suppression in a long-term field experiment where continuous application of bio-organic fertilizers (BFs) triggered disease suppressiveness when compared to chemical fertilizer application. We further demonstrated in a glasshouse experiment that the suppressiveness of the rhizosphere bacterial communities was triggered mainly by changes in community composition rather than only by the abundance of the introduced biocontrol strain. Metagenomics approaches revealed that members of the families Sphingomonadaceae and Xanthomonadaceae with the ability to produce secondary metabolites were enriched in the BF plant rhizosphere but only upon pathogen invasion. We experimentally validated this observation by inoculating bacterial isolates belonging to the families Sphingomonadaceae and Xanthomonadaceae into conducive soil, which led to a significant reduction in pathogen abundance and increase in nonribosomal peptide synthetase gene abundance. We conclude that priming of the soil microbiome with BF amendment fostered reactive bacterial communities in the rhizosphere of tomato plants in response to biotic disturbance.
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Affiliation(s)
- Xuhui Deng
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9747AG, the Netherlands
| | - Na Zhang
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yuchan Li
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chengzhi Zhu
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Baoyuan Qu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Hongjun Liu
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Rong Li
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Qirong Shen
- Jiangsu Provincial Key Laboratory of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Joana Falcao Salles
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9747AG, the Netherlands
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92
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Sha H, Li L, Lu J, Xiong J. High nutrient induces virulence in the AHPND-causing Vibrio parahaemolyticus, interpretation from the ecological assembly of shrimp gut microbiota. FISH & SHELLFISH IMMUNOLOGY 2022; 127:758-765. [PMID: 35835385 DOI: 10.1016/j.fsi.2022.07.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/03/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Shrimp diseases frequently occur during the later farming stages, when the rearing water is eutrophic. This observation provides clue that the virulence of pathogens could be induced by elevated nutrient, whereas the underlying ecological mechanism remains limited. To address this pressing knowledge, we explored how gut microbiota responded to the infection of oligotrophic (OVp) or eutrophic (EVp) pre-cultured Vibrio parahaemolyticus, a causing pathogen of shrimp acute hepatopancreatic necrosis disease (AHPND). Resulted revealed that OVp and EVp infections caused dysbiosis in the gut microbiota and compromised shrimp immunity, while the later infection led to earlier and higher mortality. Significant associations were detected between the gut microbiota and each of the measured immune activities. Neutral community model showed that the assembly of gut microbiota was more strongly governed by deterministic processes in EVp infection, followed by EVp infected and control shrimp. Additionally, there were significantly lower temporal turnover rate and average variation degree in the gut microbiota in EVp infected shrimp compared with control individuals. Notably, we identified 22 infection-discriminatory taxa after ruling out the ontogenic effect. Using profiles of the 22 indicators as independent variables, the diagnosis model accurately distinguished (an overall 85.9% accuracy) the infected status (control, OVp or EVp infected shrimp), with 81.3% accuracy at the initial infection stage. The convergent and deterministic gut microbiota in EVp infected shrimp could partially explain why it is challenge to cure APHND from an ecological viewpoint. In addition, we provided a sensitive approach for diagnosing the onset of infection, when disease symptom is unobservable.
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Affiliation(s)
- Haonan Sha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Luyue Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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93
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Dai W, Ye J, Liu S, Chang G, Xu H, Lin Z, Xue Q. Bacterial Community Dynamics in Kumamoto Oyster Crassostrea sikamea Hatchery During Larval Development. Front Microbiol 2022; 13:933941. [PMID: 35903470 PMCID: PMC9315157 DOI: 10.3389/fmicb.2022.933941] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing evidence indicates that microbes colonized in early life stages have a long-term effect on animal wellbeing in later life stages. Related research is still limited in aquatic animals, particularly in bivalve mollusks. In this study, we analyzed the dynamics of the bacterial composition of the pelagic larval stages (fertilized egg, trochophore, D-stage, veliger, and pediveliger) and the sessile postlarval stage (spat) of Kumamoto oyster (Crassostrea sikamea) and their relationships with the rearing water bacterioplankton in a hatchery by using Illumina sequencing of bacterial 16S rRNA gene. Both bacterioplankton and larval bacterial communities changed greatly over larval development, and the two communities remarkably differed (r = 0.956, P < 0.001), as highlighted by the differences in the dominant taxa and bacterial diversity. Ecological processes of larval bacterial communities were measured by abundance-unweighted and abundance-weighted standardized effect sizes of the mean nearest taxon distance (ses.MNTD). The unweighted ses.MNTD analysis revealed that the deterministic process constrained the larval bacterial assembly, whereas the weighted ses.MNTD analysis showed that larval bacterial composition was initially governed by stochasticity and then gradually by determinism in the later stages. SourceTracker analysis revealed that the larval bacteria were primarily derived from an internal source, mainly from larvae at the present stage. Additionally, the abundances of larval bacterial-mediated functional pathways that were involved in the amino acid, energy, lipid and carbohydrate metabolisms significantly altered with the larval development. These findings suggest that bacteria assemble into distinct communities in larvae and rearing water in the hatchery system, and the dynamics of bacterial community composition in larvae is likely associated with larval developmental stages.
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Affiliation(s)
- Wenfang Dai
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Jing Ye
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Sheng Liu
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Guangqiu Chang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Hongqiang Xu
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Zhihua Lin
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Qinggang Xue
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- Zhejiang Key Laboratory of Aquatic Germplasm Resource, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
- *Correspondence: Qinggang Xue
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94
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Wang H, Wu C, Zhang H, Xiao M, Ge T, Zhou Z, Liu Y, Peng S, Peng P, Chen J. Characterization of the belowground microbial community and co-occurrence networks of tobacco plants infected with bacterial wilt disease. World J Microbiol Biotechnol 2022; 38:155. [PMID: 35796795 DOI: 10.1007/s11274-022-03347-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/23/2022] [Indexed: 11/25/2022]
Abstract
Characterizing the microbial communities associated with soil-borne disease incidence is a key approach in understanding the potential role of microbes in protecting crops from pathogens. In this study, we compared the soil properties and microbial composition of the rhizosphere soil and roots of healthy and bacterial wilt-infected tobacco plants to assess their potential influence on plant health. Our results revealed that the relative abundance of pathogens was higher in diseased plants than in healthy plants. Moreover, compared with healthy plants, there was a significantly higher microbial alpha diversity in the roots and rhizosphere soil of diseased plants. In addition, we detected a lower abundance of certain plant microbiota, including species in the genera Penicillium, Trichoderma, and Burkholderia in the rhizosphere of diseased plants, which were found to be significantly negatively associated with the relative abundance of Ralstonia. Indeed, compared with healthy plants, the co-occurrence networks of diseased plants included a larger number of associations linked to plant health. Furthermore, structural equation modeling revealed that these specific microbes were correlated with disease suppression, thereby implying that they may play important roles in maintaining plant health. In conclusion, our findings provide important insights into the relationships between soil-borne disease incidence and changes in the belowground microbial community. These findings will serve as a basis for further research investigating the use of specific plant-associated genera to inhibit soil-borne diseases.
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Affiliation(s)
- Haiting Wang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha, 410004, Hunan, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Chuanfa Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Haoqing Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Mouliang Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Tida Ge
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha, 410004, Hunan, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
| | - Zhicheng Zhou
- Tobacco Research Institute of Hunan Province, Changsha, 410004, China
| | - Yongjun Liu
- Tobacco Research Institute of Hunan Province, Changsha, 410004, China
| | - Shuguang Peng
- Tobacco Research Institute of Hunan Province, Changsha, 410004, China
| | - Peiqin Peng
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha, 410004, Hunan, China.
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China.
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95
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Pan D, Xu Y, Ni Y, Zhang H, Hua R, Wu X. The efficient persistence and migration of Cupriavidus gilardii T1 contribute to the removal of MCPA in laboratory and field soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 304:119220. [PMID: 35358633 DOI: 10.1016/j.envpol.2022.119220] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
The application of exogenous biodegradation strains in pesticide-polluted soils encounters the challenges of migration and persistence of inoculants. In this study, the degradation characteristics, vertical migration capacity, and microbial ecological risk assessment of an enhanced green fluorescent protein (EGFP)-tagged 2-Methyl-4-chlorophenoxyacetic acid (MCPA)-degrading strain Cupriavidus gilardii T1 (EGFP) were investigated in the laboratory and field soils. The optimum remediation conditions for T1 (EGFP) was characterized in soils. Meanwhile, leaching experiments showed that T1 (EGFP) migrated vertically downwards in soil and contribute to the degradation of MCPA at different depths. After inoculation with T1 (EGFP), a high expression levels of EGFP gene was observed at 28 d in the laboratory soil and at 45 d in the field soil. The degradation rates of MCPA were ≥ 60% in the laboratory soil and ≥ 48% in the field soil, indicating that T1 (EGFP) can efficiently and continuously remove MCPA in both laboratory and field conditions. In addition, the inoculation of T1 (EGFP) not only showed no significant impact on the soil microbial community structure but also can alleviate the negative effects induced by MCPA to some extent. Overall, our findings suggested that T1 (EGFP) strain is an ecologically safe resource for the in situ bioremediation of MCPA-contaminated soils.
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Affiliation(s)
- Dandan Pan
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei, 230036, China
| | - Yue Xu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China
| | - Yaxin Ni
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China
| | - Houpu Zhang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei, 230036, China
| | - Rimao Hua
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei, 230036, China
| | - Xiangwei Wu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei, 230036, China.
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96
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Isenring J, Stevens MJA, Jans C, Lacroix C, Geirnaert A. Identification of Valerate as Carrying Capacity Modulator by Analyzing Lactiplantibacillus plantarum Colonization of Colonic Microbiota in vitro. Front Microbiol 2022; 13:910609. [PMID: 35722334 PMCID: PMC9197689 DOI: 10.3389/fmicb.2022.910609] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Humans ingest many microorganisms, which may colonize and interact with the resident gut microbiota. However, extensive knowledge about host-independent microbe-microbe interactions is lacking. Here, we investigated such colonization process using a derivative of the model probiotic Lactiplantibacillus plantarum WCFS1 into continuously cultivated gut microbiota in the intestinal PolyFermS fermentation model inoculated with five independently immobilized human adult fecal microbiota. L. plantarum successfully colonized and organized itself spatially in the planktonic, that is, the reactor effluent, and sessile, that is, reactor biofilm, fractions of distinct human adult microbiota. The microbiota carrying capacity for L. plantarum was independent of L. plantarum introduction dose and second supplementation. Adult microbiota (n = 3) dominated by Prevotella and Ruminoccocus exhibited a higher carrying capacity than microbiota (n = 2) dominated by Bacteroides with 105 and 103 CFU/ml of L. plantarum, respectively. Cultivation of human adult microbiota over 3 months resulted in decreased carrying capacity and correlated positively with richness and evenness, suggesting enhanced resistance toward colonizers. Our analyses ultimately allowed us to identify the fermentation metabolite valerate as a modulator to increase the carrying capacity in a microbiota-independent manner. In conclusion, by uncoupling microbe-microbe interactions from host factors, we showed that L. plantarum colonizes the in vitro colonic community in a microbiota-dependent manner. We were further able to demonstrate that L. plantarum colonization levels were not susceptible to the introduction parameters dose and repeated administration but to microbiota features. Such knowledge is relevant in gaining a deeper ecological understanding of colonizer-microbiota interactions and developing robust probiotic strategies.
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Affiliation(s)
- Julia Isenring
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Marc J A Stevens
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland.,Institute for Food Hygiene and Safety, University of Zürich, Zürich, Switzerland
| | - Christoph Jans
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
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97
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Alterations in Epiphytic Bacterial Communities during the Occurrence of Green Rot Disease in Saccharina japonica Seedlings. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bacteria are one of the causes of green rot disease (GRD) in Saccharina japonica mariculture, which may lead to complete failure of seedling production. However, the association between bacterial community and host disease severity remains largely unknown. Therefore, in this study, the bacterial communities associated with GRD-infected seedlings with naturally varying disease severity from two seedling hatcheries in Northern China were analyzed to investigate the interactions between bacterial communities and GRD. The results indicated incorrect nutrient supply in both sites. Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes were prevalent in all samples. Significant structural alterations were detected for epibacterial communities, which were further evidenced by differently abundant bacterial taxa associated with seedlings with varying disease severity. The predicted pathways of bacterial adhesion and antimicrobial compounds biosynthesis were significantly enriched in less severely diseased seedlings, whereas glutathione metabolism and lipopolysaccharide biosynthesis were significantly increased in more severely diseased seedlings. The predicted categories of a two-component system, flagellar assembly, bacterial chemotaxis, and biofilm formation were significantly enriched in the bacterioplankton in more severely infected seawater. The differential bacterial community compositions and predicted functions provide new clues to elucidate the mechanism underlying the interaction between GRD occurrence and bacterial communities.
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98
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Bziuk N, Maccario L, Sørensen SJ, Schikora A, Smalla K. Barley Rhizosphere Microbiome Transplantation – A Strategy to Decrease Susceptibility of Barley Grown in Soils With Low Microbial Diversity to Powdery Mildew. Front Microbiol 2022; 13:830905. [PMID: 35685930 PMCID: PMC9173696 DOI: 10.3389/fmicb.2022.830905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/26/2022] [Indexed: 11/23/2022] Open
Abstract
Beneficial bacteria in the rhizosphere are known to trigger faster and stronger plant immune responses to biotic and abiotic stressors. In the present study, we aimed to test the hypothesis that a rhizosphere microbiome transplant (RMT) may improve the immune response and reduce the disease rates of barley (Hordeum vulgare). This hypothesis was tested in a greenhouse system with the powdery mildew-causing fungus Blumeria graminis f. sp. hordei (Bgh). Detached rhizosphere microbiome from barley grown in a field soil was transplanted to barley seedlings grown in potting soil with reduced microbial diversity. Saline-treated plants served as control. At the three-leaf stage, barley was infected with Bgh. Decreased susceptibility to Bgh was observed for barley treated with the RMT as displayed by lower Bgh pustule counts in a detached leaf assay. A trend toward enhanced relative transcript abundances of the defense-related genes PR1b and PR17b was observed in leaves, 24 h after the Bgh challenge, when compared to the control. Moreover, 10 days after the Bgh challenge, the barley rhizosphere microbiome was harvested and analyzed by sequencing of 16S rRNA gene amplicons. The microbial community composition was significantly influenced by the RMT and displayed higher microbial diversity compared to the control. Furthermore, microbial beta-diversity and predicted functional profiles revealed a treatment-dependent clustering. Bacterial isolates from the RMT showed in vitro plant beneficial traits related to induced resistance. Our results showed that transplantation of a rhizosphere microbiome could be a sustainable strategy to improve the health of plants grown in potting soil with low microbial diversity under greenhouse conditions.
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Affiliation(s)
- Nina Bziuk
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Lorrie Maccario
- Section of Microbiology, Copenhagen University, Copenhagen, Denmark
| | | | - Adam Schikora
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- *Correspondence: Kornelia Smalla,
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99
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Bacterial Composition and Interactions in Raw Milk and Teat Skin of Dairy Cows. FERMENTATION 2022. [DOI: 10.3390/fermentation8050235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The microbiota in raw milk plays an important role in the health of dairy cows and the safety of dairy products, which might be influenced by that in teat skin. However, the microbiota composition in raw milk and teat skin, as well as the bacterial interaction between the two adjacent spatial locations, remains elusive. Here, we investigated the composition, diversity, and co-occurrence network of the bacterial communities in raw milk and on teat skin, as well as the shift of bacterial communities during the teat bath using 469 samples from 156 individual cows. We observed that raw milk and teat skin harbored significantly different bacterial communities according to an assessment of the genera numbers (p < 0.05) and PCoA analysis (ANOSIM p < 0.05). The microbiota in raw milk was dominated by Proteobacteria (58.5% in relative abundance) at the phylum level and by Pseudomonas (51.2%) at the genus level, while that in teat skin was dominated by Firmicutes (46.9%) at the phylum level and by Pseudomonas (11.0%) at the genus level. We observed a massive difference between the bacterial subnetworks in raw milk and teat, and the bacterial abundance in these two adjacent spatial locations was positively correlated (p < 0.05). Using Bayesian algorithms, we identified that 92.1% of bacteria in raw milk were transferred from teat skin, while 63.6% of bacteria on teat skin were transferred from raw milk. Moreover, microbiota composition in teat skin could be affected by the teat bath with iodine disinfectant, which tended to be more similar to that in raw milk after the teat bath (p < 0.05), while the abundance of the dominant genus Pseudomonas significantly increased (p < 0.05). These findings expand our knowledge on the microbiota composition in teat skin and raw milk, as well as the interaction between these two adjacent spatial locations.
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100
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Yang LY, Zhou SYD, Lin CS, Huang XR, Neilson R, Yang XR. Effects of biofertilizer on soil microbial diversity and antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153170. [PMID: 35051473 DOI: 10.1016/j.scitotenv.2022.153170] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Spread of antibiotic resistance or the presence of antibiotic resistance genes (ARGs) in pathogens is a globally recognized threat to human health. Numerous studies have shown that application of organic fertilizers may increase the risk of ARGs, however, the risk of resistance genes associated with biofertilizers is largely unknown. To investigate whether biofertilizer application introduces ARGs to the soil, we used high-throughput quantitative polymerization chain reaction (HT-qPCR) to explore the effect of biofertilizer application over three years on soil ARGs in three orchards with different locations in China. Redundancy analysis showed specific and significant differences in the beta diversity of soil bacteria and fungi between treatments (fertilizer vs. no fertilizer). One-way ANOVA analysis revealed findings of the main driver of the significant difference in microbial community structure between fertilizer and control treatment was the change in soil properties following the application of biofertilizer. A total of 139 ARGs and 27 MGEs (mobile genetic elements), and 46 ARGs and 6 MGEs from 11 major taxa were detected in biofertilizer and soil samples, respectively. Only the samples from Guangxi had significant differences in the detected number of ARGs and MGEs between fertilization and control. Through structural equation modeling (SEM), we found that soil properties indirectly affected ARGs by shaping bacterial diversity, while bacterial abundance directly affected ARGs. Biofertilizer application did not significantly alter the relative abundance of ARGs in soil due to the complexity of the soil environment and competition between exogenous and native microorganisms. This study provided new insights into the spread of the antibiotic resistome of the soil through biofertilizer applications.
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Affiliation(s)
- Le-Yang Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Shu-Yi-Dan Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Chen-Shuo Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Rong Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; College of Life Sciences, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou 350002, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, UK
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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