1
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Abbasi E, Akçay E. Host control and species interactions jointly determine microbiome community structure. Theor Popul Biol 2024; 158:185-194. [PMID: 38925487 DOI: 10.1016/j.tpb.2024.06.006] [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: 02/26/2023] [Revised: 03/21/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
The host microbiome can be considered an ecological community of microbes present inside a complex and dynamic host environment. The host is under selective pressure to ensure that its microbiome remains beneficial. The host can impose a range of ecological filters including the immune response that can influence the assembly and composition of the microbial community. How the host immune response interacts with the within-microbiome community dynamics to affect the assembly of the microbiome has been largely unexplored. We present here a mathematical framework to elucidate the role of host immune response and its interaction with the balance of ecological interactions types within the microbiome community. We find that highly mutualistic microbial communities characteristic of high community density are most susceptible to changes in immune control and become invasion prone as host immune control strength is increased. Whereas highly competitive communities remain relatively stable in resisting invasion to changing host immune control. Our model reveals that the host immune control can interact in unexpected ways with a microbial community depending on the prevalent ecological interactions types for that community. We stress the need to incorporate the role of host-control mechanisms to better understand microbiome community assembly and stability.
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Affiliation(s)
- Eeman Abbasi
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104, USA.
| | - Erol Akçay
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104, USA
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2
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Wang N, Ding D, Zhang H, Ding X, Zhang D, Yao C, Fan X, Ding R, Wang H, Jiang T. Anthropogenic activity shapes the assemble and co-occurrence pattern of microbial communities in fishing harbors around the Bohai Economic Circle. ENVIRONMENTAL RESEARCH 2024; 259:119563. [PMID: 38971358 DOI: 10.1016/j.envres.2024.119563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/25/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
This study aimed to elucidate the effects of coastal environmental stress on the composition of sediment bacterial communities and their cooccurrence patterns in fishing harbors around the Bohai Economic Circle, China. Compared with the natural sea area, fishing harbors contained higher levels of organic pollution (organic pollution index = 0.12±0.026) and considerably reduced bacterial richness and evenness. The distributions of sediment microbial communities clustered along the pollutant concentration gradients across fishing harbors. Betaproteobacteria dominated (76%) organically polluted fishing harbors, which were mostly disturbed by anthropogenic activities. However, the harbors also revealed the absence of numerous pathogenic (Coxiella and Legionella) and photosynthetic (Synechococcus and Leptolyngbya) bacteria. Abundant genera, including Thiobacillus and Arenimonas, exhibited a positive correlation with total phosphorus and a negative correlation with total nitrogen in sediments. Meanwhile, Sulfurovum, Psychrobacter, and Woeseia showed the opposite trend. Pollutant accumulation and anthropogenic activities caused the decrease in the sediment microbial diversity and dispersal ability and promoted convergent evolution. Severely polluted harbors with simplified cooccurrence networks revealed the presence of destabilized microbial communities. In addition, the modularity of bacterial networks decreased with organic pollution. Our results provide important insights into the adjustment mechanism of microbial communities to community organization and functions under environmental pollution stress. Overall, this study enhanced our understanding of how microbial communities in coastal sediments adapted and survived amidst anthropogenic activities like oily effluent discharges from large ships, wash water, domestic sewage, garbage, and fisheries wastes. It also examined their resilience to future contamination.
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Affiliation(s)
- Nan Wang
- School of Ocean, Yantai University, Yantai 264005, China
| | - Dongsheng Ding
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Huihui Zhang
- School of Ocean, Yantai University, Yantai 264005, China
| | - Xiaokun Ding
- School of Ocean, Yantai University, Yantai 264005, China
| | - Di Zhang
- School of Ocean, Yantai University, Yantai 264005, China
| | - Chenghao Yao
- Shandong Hongxin Environmental Protection Technology Co., Ltd
| | - Xiao Fan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - RenYe Ding
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Hualong Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao, 266003, China.
| | - Tao Jiang
- School of Ocean, Yantai University, Yantai 264005, China.
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3
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Zhu Y, Momeni B. Revisiting the invasion paradox: Resistance-richness relationship is driven by augmentation and displacement trends. PLoS Comput Biol 2024; 20:e1012193. [PMID: 38865380 PMCID: PMC11198907 DOI: 10.1371/journal.pcbi.1012193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/25/2024] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Host-associated resident microbiota can protect their host from pathogens-a community-level trait called colonization resistance. The effect of the diversity of the resident community in previous studies has shown contradictory results, with higher diversity either strengthening or weakening colonization resistance. To control the confounding factors that may lead to such contradictions, we use mathematical simulations with a focus on species interactions and their impact on colonization resistance. We use a mediator-explicit model that accounts for metabolite-mediated interactions to perform in silico invasion experiments. We show that the relationship between colonization resistance and species richness of the resident community is not monotonic because it depends on two underlying trends as the richness of the resident community increases: a decrease in instances of augmentation (invader species added, without driving out resident species) and an increase in instances of displacement (invader species added, driving out some of the resident species). These trends hold consistently under different parameters, regardless of the number of compounds that mediate interactions between species or the proportion of the facilitative versus inhibitory interactions among species. Our results show a positive correlation between resistance and diversity in low-richness communities and a negative correlation in high-richness communities, offering an explanation for the seemingly contradictory trend in the resistance-diversity relationship in previous reports.
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Affiliation(s)
- Yu Zhu
- Biology Department, Boston College, Chestnut Hill, Massachusetts, Unites States of America
| | - Babak Momeni
- Biology Department, Boston College, Chestnut Hill, Massachusetts, Unites States of America
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4
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Vandermaesen J, Daly AJ, Mawarda PC, Baetens JM, De Baets B, Boon N, Springael D. Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship. Ecol Lett 2024; 27:e14433. [PMID: 38712704 DOI: 10.1111/ele.14433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024]
Abstract
The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.
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Affiliation(s)
| | - Aisling J Daly
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Panji Cahya Mawarda
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
- Research Center for Applied Microbiology, National Research and Innovation Agency Republic of Indonesia (BRIN), Bandung, Indonesia
| | - Jan M Baetens
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Bernard De Baets
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Gent, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
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5
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Čaušević S, Dubey M, Morales M, Salazar G, Sentchilo V, Carraro N, Ruscheweyh HJ, Sunagawa S, van der Meer JR. Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions. Nat Commun 2024; 15:2557. [PMID: 38519488 PMCID: PMC10959995 DOI: 10.1038/s41467-024-46933-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/13/2024] [Indexed: 03/25/2024] Open
Abstract
Microbiome engineering - the targeted manipulation of microbial communities - is considered a promising strategy to restore ecosystems, but experimental support and mechanistic understanding are required. Here, we show that bacterial inoculants for soil microbiome engineering may fail to establish because they inadvertently facilitate growth of native resident microbiomes. By generating soil microcosms in presence or absence of standardized soil resident communities, we show how different nutrient availabilities limit outgrowth of focal bacterial inoculants (three Pseudomonads), and how this might be improved by adding an artificial, inoculant-selective nutrient niche. Through random paired interaction assays in agarose micro-beads, we demonstrate that, in addition to direct competition, inoculants lose competitiveness by facilitating growth of resident soil bacteria. Metatranscriptomics experiments with toluene as selective nutrient niche for the inoculant Pseudomonas veronii indicate that this facilitation is due to loss and uptake of excreted metabolites by resident taxa. Generation of selective nutrient niches for inoculants may help to favor their proliferation for the duration of their intended action while limiting their competitive loss.
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Affiliation(s)
- Senka Čaušević
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Marian Morales
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Guillem Salazar
- Department of Biology Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
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6
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Guo Z, Zhang J, Liu Z, Li Y, Li M, Meng Q, Yang Z, Luo Y, Zhang Q, Yan M. Trichoderma harzianum prevents red kidney bean root rot by increasing plant antioxidant enzyme activity and regulating the rhizosphere microbial community. Front Microbiol 2024; 15:1348680. [PMID: 38572240 PMCID: PMC10987954 DOI: 10.3389/fmicb.2024.1348680] [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: 12/03/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024] Open
Abstract
Root rot is one of the main reasons for yield losses of red kidney bean (Phaseolus vulgaris) production. Pre-inoculation with Trichoderma harzianum can effectively lower the incidence of red kidney bean root rot. In this study, four treatments including CK (control), Fu13 (Fusarium oxysporum), T891 (T. harzianum) and T891 + Fu13 (T. harzianum + F. oxysporum) were arranged in a pot experiment to investigate how T891 affected the incidence and severity of root rot, plant growth, and changes of defense enzyme activity in red kidney bean plants. Community composition and diversity of the rhizosphere microbiota was evaluated through high-throughput sequencing, and co-occurrence network was analyzed. The results showed that when compared to the Fu13 treatment, pre-inoculation with T891 reduced the incidence and severity of red kidney bean root rot by 40.62 and 68.03% (p < 0.05), increased the root length, shoot length, total dry biomass by 48.63, 97.72, 122.17%. Upregulated activity of super-oxide dismutase (SOD), peroxidase (POD), catalase (CAT) by 7.32, 38.48, 98.31% (p < 0.05), and reduced malondialdehyde (MDA) by 23.70% (p < 0.05), respectively. Microbiological analyses also showed that F. oxysporum reduced alpha diversity resulting in alteration the composition of the rhizosphere microbial community in red kidney bean. T891 significantly reduced abundance of F. oxysporum, allowing the enrichment of potentially beneficial bacteria Porphyrobacter (ASV 46), Lysobacter (ASV 85), Microbacteriaceae (ASV 105), and Gemmatimonas (ASV 107), resulting in a more stable structure of the microbial network. The results of random forest analysis further revealed that ASV 46 (Porphyrobacter) was the primary influencing factor for the incidence of root rot after inoculation with T891, while ASV 85 (Lysobacter) was the primary influencing factor for the biomass of red kidney bean. In conclusion, T. harzianum promotes the growth of red kidney bean and inhibits root rot by improving plant antioxidant enzyme activity and regulating the rhizosphere microbial community.
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Affiliation(s)
- Zhifen Guo
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan, China
| | - Jiaxing Zhang
- Key Laboratory for Soil Environment and Nutrient Resources, Taiyuan, Shanxi, China
- Institute of Eco-Environment and Industrial Technology, Shanxi Agricultural University, Taiyuan, China
| | - Zhibin Liu
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan, China
| | - Yu Li
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan, China
| | - Meng Li
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan, China
| | - Qiuxia Meng
- Key Laboratory for Soil Environment and Nutrient Resources, Taiyuan, Shanxi, China
- Institute of Eco-Environment and Industrial Technology, Shanxi Agricultural University, Taiyuan, China
| | - Zhiping Yang
- Key Laboratory for Soil Environment and Nutrient Resources, Taiyuan, Shanxi, China
- Institute of Eco-Environment and Industrial Technology, Shanxi Agricultural University, Taiyuan, China
| | - Yuan Luo
- Institute of Eco-Environment and Industrial Technology, Shanxi Agricultural University, Taiyuan, China
| | - Qiang Zhang
- Shanxi Agricultural University, Taiyuan, China
| | - Min Yan
- Key Laboratory for Soil Environment and Nutrient Resources, Taiyuan, Shanxi, China
- Institute of Eco-Environment and Industrial Technology, Shanxi Agricultural University, Taiyuan, China
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7
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Papin M, Philippot L, Breuil MC, Bru D, Dreux-Zigha A, Mounier A, Le Roux X, Rouard N, Spor A. Survival of a microbial inoculant in soil after recurrent inoculations. Sci Rep 2024; 14:4177. [PMID: 38378706 PMCID: PMC10879113 DOI: 10.1038/s41598-024-54069-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (106 and 108 cfu.g soil-1). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.
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Affiliation(s)
- M Papin
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - L Philippot
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France.
| | - M C Breuil
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - D Bru
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - A Dreux-Zigha
- GreenCell Biopole Clermont Limagne, 63360, St Beauzire, France
| | - A Mounier
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - X Le Roux
- Universite Claude Bernard Lyon 1, Microbial Ecology Centre LEM, INRAE, CNRS, VetAgroSup, UMR INRAE 1418, 43 Blvd 11 Novembre 1918, 69622, Villeurbanne, France
| | - N Rouard
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
| | - A Spor
- Univ Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, 17 Rue Sully, 21000, Dijon, France
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8
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Van Gerrewey T, Navarrete O, Vandecruys M, Perneel M, Boon N, Geelen D. Bacterially enhanced plant-growing media for controlled environment agriculture. Microb Biotechnol 2024; 17:e14422. [PMID: 38380980 PMCID: PMC10880579 DOI: 10.1111/1751-7915.14422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/22/2024] Open
Abstract
Microbe-plant interactions in the root zone not only shape crop performance in soil but also in hydroponic cultivation systems. The biological and physicochemical properties of the plant-growing medium determine the root-associated microbial community and influence bacterial inoculation effectiveness, which affects plant growth. This study investigated the combined impact of plant-growing media composition and bacterial community inoculation on the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Ten plant-growing media were composed of varying raw materials, including black peat, white peat, coir pith, wood fibre, composted bark, green waste compost, perlite and sand. In addition, five different bacterial community inocula (BCI S1-5) were collected from the roots of lettuce obtained at different farms. After inoculation and cultivation inside a vertical farm, lettuce root-associated bacterial community structures, diversity and compositions were determined by evaluating 16S rRNA gene sequences. The study revealed distinct bacterial community structures among experimental replicates, highlighting the influence of raw material variations on root-associated bacterial communities, even at the batch level. However, bacterial community inoculation allowed modulation of the root-associated bacterial communities independently from the plant-growing medium composition. Bacterial diversity was identified as a key determinant of plant growth performance with green waste compost introducing Bacilli and Actinobacteria, and bacterial community inoculum S3 introducing Pseudomonas, which positively correlated with plant growth. These findings challenge the prevailing notion of hydroponic cultivation systems as sterile environments and highlight the significance of proper plant-growing media raw material selection and bacterial community inoculation in shaping root-associated microbiomes that provide stability through microbial diversity. This study supports the concept of creating bacterially enhanced plant-growing media to promote plant growth in controlled environment agriculture.
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Affiliation(s)
- Thijs Van Gerrewey
- HortiCell, Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
- Urban Crop Solutions BVBAWaregemBelgium
- Agaris Belgium NVGentBelgium
| | | | | | - Maaike Perneel
- Cropfit, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
| | - Danny Geelen
- HortiCell, Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
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9
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Emmenegger B, Massoni J, Pestalozzi CM, Bortfeld-Miller M, Maier BA, Vorholt JA. Identifying microbiota community patterns important for plant protection using synthetic communities and machine learning. Nat Commun 2023; 14:7983. [PMID: 38042924 PMCID: PMC10693592 DOI: 10.1038/s41467-023-43793-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: 06/20/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023] Open
Abstract
Plant-associated microbiomes contribute to important ecosystem functions such as host resistance to biotic and abiotic stresses. The factors that determine such community outcomes are inherently difficult to identify under complex environmental conditions. In this study, we present an experimental and analytical approach to explore microbiota properties relevant for a microbiota-conferred host phenotype, here plant protection, in a reductionist system. We screened 136 randomly assembled synthetic communities (SynComs) of five bacterial strains each, followed by classification and regression analyses as well as empirical validation to test potential explanatory factors of community structure and composition, including evenness, total commensal colonization, phylogenetic diversity, and strain identity. We find strain identity to be the most important predictor of pathogen reduction, with machine learning algorithms improving performances compared to random classifications (94-100% versus 32% recall) and non-modelled predictions (0.79-1.06 versus 1.5 RMSE). Further experimental validation confirms three strains as the main drivers of pathogen reduction and two additional strains that confer protection in combination. Beyond the specific application presented in our study, we provide a framework that can be adapted to help determine features relevant for microbiota function in other biological systems.
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Affiliation(s)
| | - Julien Massoni
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
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10
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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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11
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Wu B, Guan X, Deng T, Yang X, Li J, Zhou M, Wang C, Wang S, Yan Q, Shu L, He Q, He Z. Synthetic Denitrifying Communities Reveal a Positive and Dynamic Biodiversity-Ecosystem Functioning Relationship during Experimental Evolution. Microbiol Spectr 2023; 11:e0452822. [PMID: 37154752 PMCID: PMC10269844 DOI: 10.1128/spectrum.04528-22] [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: 11/07/2022] [Accepted: 04/04/2023] [Indexed: 05/10/2023] Open
Abstract
Biodiversity is vital for ecosystem functions and services, and many studies have reported positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships in plant and animal systems. However, if the BEF relationship exists and how it evolves remains elusive in microbial systems. Here, we selected 12 Shewanella denitrifiers to construct synthetic denitrifying communities (SDCs) with a richness gradient spanning 1 to 12 species, which were subjected to approximately 180 days (with 60 transfers) of experimental evolution with generational changes in community functions continuously tracked. A significant positive correlation was observed between community richness and functions, represented by productivity (biomass) and denitrification rate, however, such a positive correlation was transient, only significant in earlier days (0 to 60) during the evolution experiment (180 days). Also, we found that community functions generally increased throughout the evolution experiment. Furthermore, microbial community functions with lower richness exhibited greater increases than those with higher richness. Biodiversity effect analysis revealed positive BEF relationships largely attributable to complementary effects, which were more pronounced in communities with lower richness than those with higher richness. This study is one of the first studies that advances our understanding of BEF relationships and their evolutionary mechanisms in microbial systems, highlighting the crucial role of evolution in predicting the BEF relationship in microbial systems. IMPORTANCE Despite the consensus that biodiversity supports ecosystem functioning, not all experimental models of macro-organisms support this notion with positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships reported. The fast-growing, metabolically versatile, and easy manipulation nature of microbial communities allows us to explore well the BEF relationship and further interrogate if the BEF relationship remains constant during long-term community evolution. Here, we constructed multiple synthetic denitrifying communities (SDCs) by randomly selecting species from a candidate pool of 12 Shewanella denitrifiers. These SDCs differ in species richness, spanning 1 to 12 species, and were monitored continuously for community functional shifts during approximately 180-day parallel cultivation. We demonstrated that the BEF relationship was dynamic with initially (day 0 to 60) greater productivity and denitrification among SDCs of higher richness. However, such pattern was reversed thereafter with greater productivity and denitrification increments in lower-richness SDCs, likely due to a greater accumulation of beneficial mutations during the experimental evolution.
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Affiliation(s)
- Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Min Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Tennessee, USA
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
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12
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Jiang M, Delgado-Baquerizo M, Yuan MM, Ding J, Yergeau E, Zhou J, Crowther TW, Liang Y. Home-based microbial solution to boost crop growth in low-fertility soil. THE NEW PHYTOLOGIST 2023. [PMID: 37149890 DOI: 10.1111/nph.18943] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
Soil microbial inoculants are expected to boost crop productivity under climate change and soil degradation. However, the efficiency of native vs commercialized microbial inoculants in soils with different fertility and impacts on resident microbial communities remain unclear. We investigated the differential plant growth responses to native synthetic microbial community (SynCom) and commercial plant growth-promoting rhizobacteria (PGPR). We quantified the microbial colonization and dynamic of niche structure to emphasize the home-field advantages for native microbial inoculants. A native SynCom of 21 bacterial strains, originating from three typical agricultural soils, conferred a special advantage in promoting maize growth under low-fertility conditions. The root : shoot ratio of fresh weight increased by 78-121% with SynCom but only 23-86% with PGPRs. This phenotype correlated with the potential robust colonization of SynCom and positive interactions with the resident community. Niche breadth analysis revealed that SynCom inoculation induced a neutral disturbance to the niche structure. However, even PGPRs failed to colonize the natural soil, they decreased niche breadth and increased niche overlap by 59.2-62.4%, exacerbating competition. These results suggest that the home-field advantage of native microbes may serve as a basis for engineering crop microbiomes to support food production in widely distributed poor soils.
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Affiliation(s)
- Meitong Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Ave Reina Mercedes 10, E-41012, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Jixian Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Etienne Yergeau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, H7V 1B7, Québec, Canada
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zurich, Zurich, 8092, Switzerland
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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13
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Zhao W, Ban Y, Su Z, Li S, Liu X, Guo Q, Ma P. Colonization Ability of Bacillus subtilis NCD-2 in Different Crops and Its Effect on Rhizosphere Microorganisms. Microorganisms 2023; 11:microorganisms11030776. [PMID: 36985349 PMCID: PMC10058285 DOI: 10.3390/microorganisms11030776] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Bacillus subtilis strain NCD-2 is a promising biocontrol agent for soil-borne plant diseases and shows potential for promoting the growth of some crops. The purposes of this study were to analyze the colonization ability of strain NCD-2 in different crops and reveal the plant growth promotion mechanism of strain NCD-2 by rhizosphere microbiome analysis. qRT-PCR was used to determine the populations of strain NCD-2, and microbial communities’ structures were analyzed through amplicon sequencing after application of strain NCD-2. Results demonstrated that strain NCD-2 had a good growth promotion effect on tomato, eggplant and pepper, and it was the most abundant in eggplant rhizosphere soil. There were significantly differences in the types of beneficial microorganisms recruited for different crops after application of strain NCD-2. PICRUSt analysis showed that the relative abundances of functional genes for amino acid transport and metabolism, coenzyme transport and metabolism, lipid transport and metabolism, inorganic ion transport and metabolism, and defense mechanisms were enriched in the rhizospheres of pepper and eggplant more than in the rhizospheres of cotton, tomato and maize after application of strain NCD-2. In summary, the colonization ability of strain NCD-2 for five plants was different. There were differences in microbial communities’ structure in rhizosphere of different plants after application of strain NCD-2. Based on the results obtained in this study, it was concluded that the growth promoting ability of strain NCD-2 were correlated with its colonization quantity and the microbial species it recruited.
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Affiliation(s)
| | | | | | | | | | - Qinggang Guo
- Correspondence: (Q.G.); (P.M.); Tel.: +86-312-5915671 (Q.G.); Tel./Fax: +86-312-5915678 (P.M.)
| | - Ping Ma
- Correspondence: (Q.G.); (P.M.); Tel.: +86-312-5915671 (Q.G.); Tel./Fax: +86-312-5915678 (P.M.)
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14
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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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15
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Mawarda PC, Mallon CA, Le Roux X, van Elsas JD, Salles JF. Interactions between Bacterial Inoculants and Native Soil Bacterial Community: the Case of Spore-forming Bacillus spp. FEMS Microbiol Ecol 2022; 98:6776013. [PMID: 36302145 PMCID: PMC9681130 DOI: 10.1093/femsec/fiac127] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/21/2022] [Accepted: 10/25/2022] [Indexed: 01/21/2023] Open
Abstract
Microbial diversity can restrict the invasion and impact of alien microbes into soils via resource competition. However, this theory has not been tested on various microbial invaders with different ecological traits, particularly spore-forming bacteria. Here we investigated the survival capacity of two introduced spore-forming bacteria, Bacillus mycoides (BM) and B. pumillus (BP) and their impact on the soil microbiome niches with low and high diversity. We hypothesized that higher soil bacterial diversity would better restrict Bacillus survival via resource competition, and the invasion would alter the resident bacterial communities' niches only if inoculants do not escape competition with the soil community (e.g. through sporulation). Our findings showed that BP could not survive as viable propagules and transiently impacted the bacterial communities' niche structure. This may be linked to its poor resource usage and low growth rate. Having better resource use capacities, BM better survived in soil, though its survival was weakly related to the remaining resources left for them by the soil community. BM strongly affected the community niche structure, ultimately in less diverse communities. These findings show that the inverse diversity-invasibility relationship can be valid for some spore-forming bacteria, but only when they have sufficient resource use capacity.
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Affiliation(s)
| | - Cyrus A Mallon
- Microbial Community Ecology Cluster, expertise group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Xavier Le Roux
- INRAE, CNRS, Université Lyon 1, Université de Lyon, VetAgroSup, Laboratoire d'Ecologie Microbienne LEM, UMR 1418 INRAE, UMR 5557 CNRS, 69622 Villeurbanne Cedex, France
| | - 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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16
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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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17
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Mukjang N, Mombrikotb SB, Bell T. Microbial community succession in steam-sterilized greenhouses infected with Fusarium oxysporum. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:577-583. [PMID: 35445561 PMCID: PMC9544407 DOI: 10.1111/1758-2229.13072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Fusarium is an economically important crop pathogen but spends a large part of its life cycle in bulk soil environments where it interacts with a diverse community of soil microbes. Antagonistic interactions (e.g. competition) between the resident microbial community and Fusarium could constrain the growth of Fusarium in soil, which might therefore slow or prevent Fusarium establishment. We tracked Fusarium oxysporum in floriculture greenhouses where the soil had been steam-sterilized to remove Fusarium. The data indicated a resurgence of soil bacteria and fungi during the first 90 days post-sterilization, followed by a rapid decline in subsequent weeks, which was associated with an increase in F. oxysporum abundance at 148 days post sterilization. These changes over time were associated with successional changes in the bacterial but not the fungal communities. The results illustrate that, although soil steaming clears Fusarium in the short term, it may exacerbate re-emergence as the resident community is continually depleted by the steaming process while Fusarium benefits from nutrients released by steaming. Observations suggest combining steaming with microbial inoculations could help reduce the recovery of Fusarium reducing the fungal load in the first instance and preventing subsequent build-up by giving a head start to its saprophytic competitors.
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Affiliation(s)
- Nilita Mukjang
- Department of Life SciencesImperial College LondonAscotBerkshireUK
| | | | - Thomas Bell
- Department of Life SciencesImperial College LondonAscotBerkshireUK
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18
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McKnight DT, Huerlimann R, Bower DS, Schwarzkopf L, Alford RA, Zenger KR. The interplay of fungal and bacterial microbiomes on rainforest frogs following a disease outbreak. Ecosphere 2022. [DOI: 10.1002/ecs2.4037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Donald T. McKnight
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Roger Huerlimann
- College of Science and Engineering James Cook University Townsville Queensland Australia
- Marine Climate Change Unit Okinawa Institute of Science and Technology Onnason Okinawa Japan
| | - Deborah S. Bower
- College of Science and Engineering James Cook University Townsville Queensland Australia
- School of Environmental and Rural Science University of New England Armidale New South Wales Australia
| | - Lin Schwarzkopf
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Ross A. Alford
- College of Science and Engineering James Cook University Townsville Queensland Australia
| | - Kyall R. Zenger
- College of Science and Engineering James Cook University Townsville Queensland Australia
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19
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Mawarda PC, Lakke SL, Dirk van Elsas J, Salles JF. Temporal dynamics of the soil bacterial community following Bacillus invasion. iScience 2022; 25:104185. [PMID: 35479409 PMCID: PMC9035691 DOI: 10.1016/j.isci.2022.104185] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 01/04/2023] Open
Abstract
Microbial inoculants are constantly introduced into the soil as the deployment of sustainable agricultural practices increases. These introductions might induce soil native communities’ dynamics, influencing their assembly process. We followed the impact and successional trajectories of native soil communities of different diversity levels to the invasion by Bacillus mycoides M2E15 (BM) and B. pumilus ECOB02 (BP). Whereas the impact was more substantial when the invader survived (BM), the transient presence of BP also exerted tangible effects on soil bacterial diversity. Community assembly analyses revealed that deterministic processes primarily drove community turnover. This selection acted stronger in highly diverse communities invaded by BM than in those invaded by BP. We showed that resident bacterial communities exhibit patterns of secondary succession following invasions, even if the latter are unsuccessful. Furthermore, the intensification of biotic interactions in more diverse communities might strengthen the deterministic selection upon invasion in communities with higher diversity. Microbial invaders altered soil bacterial diversity regardless of their survival The impact was more pronounced when the invader was established Deterministic selection primarily drove community turnover following invasion The dynamic of invaded community showed pattern of secondary succession
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20
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Howse MWF, McGruddy RA, Felden A, Baty JW, Haywood J, Lester PJ. The native and exotic prey community of two invasive paper wasps (Hymenoptera: Vespidae) in New Zealand as determined by DNA barcoding. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02739-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
AbstractSocial wasps are invasive in many regions around the world. In their new communities, introduced predators such as these wasps may be beneficial as consumers of exotic pests, but they will also consume native species. Here, we examined the diet of the exotic European paper wasp (Polistes dominula) and the closely related congener, Polistes chinensis, in a region of New Zealand where they co-occur. DNA barcoding was used to analyse their diet. The diet of both wasp species was largely Lepidopteran but other orders such as Hemiptera, Diptera and Coleoptera were also represented. Our analysis showed substantial site-to-site variation in diet. The two wasps differed significantly in their prey, although these differences appear to be driven by taxa identified from a small number of DNA reads in a small number of samples. Native and introduced fauna were represented in the diets of both wasps and included important agricultural pests. Of the 92 prey taxa able to be identified to species level, 81 were identified as exotic or introduced to New Zealand. The remaining 11 were species native to New Zealand. However, our estimates suggest over 50% of the prey DNA in the wasp diet is derived from native species. These wasps are abundant in some coastal and urban habitats, where they are likely to consume pest species as well as native species of conservation importance. The ecosystem services or costs and benefits provided by these invasive species are likely to be contingent on the prey communities and habitats they occupy.
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21
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Ferreira-Rodríguez N, Gangloff M, Shafer G, Atkinson CL. Drivers of ecosystem vulnerability to Corbicula invasions in southeastern North America. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02751-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractInvasive species introduction is one of the major ongoing ecological global crises. Identifying factors responsible for the success of invasive species is key for the implementation of effective management actions. The invasive filter-feeding bivalve, Corbicula, is of particular interest because it has become ubiquitous in many river basins across North America and elsewhere. Here we sampled bivalve assemblages, environmental indicators, and land cover parameters in the Ouachita highlands in southeastern Oklahoma and southwestern Arkansas, and in the Gulf Coastal Plain of Alabama to test three working models (using structural equation modeling, SEM) based on a priori scientific knowledge regarding Corbicula invasions. Our models tested three competing hypotheses: (1) Native mussel declines are related to land use changes at the watershed level and subsequent Corbicula colonization is a result of an empty niche; (2) Corbicula abundance is one of the factors responsible for native mussel declines and has an interactive effect with land use change at the watershed level; (3) Native mussel declines and Corbicula success are both related to land use changes at the watershed level. We found no evidence for the first two hypotheses. However, we found that environmental indicators and land cover parameters at the watershed scale were robust predictors of Corbicula abundance. In particular, agricultural land cover was positively related with Corbicula density. These results suggest that further improvement of conventional agricultural practices including the optimization of fertilizer delivery systems may represent an opportunity to manage this species by limiting nutrient inputs to stream ecosystems. Preservation of extensive floodplain habitats may help buffer these inputs by providing key ecosystem services including sediment and nutrient retention.
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22
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Albright MBN, Louca S, Winkler DE, Feeser KL, Haig SJ, Whiteson KL, Emerson JB, Dunbar J. Solutions in microbiome engineering: prioritizing barriers to organism establishment. THE ISME JOURNAL 2022; 16:331-338. [PMID: 34420034 PMCID: PMC8776856 DOI: 10.1038/s41396-021-01088-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 02/07/2023]
Abstract
Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.
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Affiliation(s)
| | - Stilianos Louca
- Department of Biology, University of Oregon, Eugene, OR, USA
| | - Daniel E Winkler
- United States Geological Survey, Southwest Biological Science Center, Moab, UT, USA
| | - Kelli L Feeser
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Sarah-Jane Haig
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Katrine L Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA
| | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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23
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Li SP, Jia P, Fan SY, Wu Y, Liu X, Meng Y, Li Y, Shu WS, Li JT, Jiang L. Functional traits explain the consistent resistance of biodiversity to plant invasion under nitrogen enrichment. Ecol Lett 2021; 25:778-789. [PMID: 34972253 DOI: 10.1111/ele.13951] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/17/2021] [Accepted: 12/02/2021] [Indexed: 01/21/2023]
Abstract
Elton's biotic resistance hypothesis, which posits that diverse communities should be more resistant to biological invasions, has received considerable experimental support. However, it remains unclear whether such a negative diversity-invasibility relationship would persist under anthropogenic environmental change. By using the common ragweed (Ambrosia artemisiifolia) as a model invader, our 4-year grassland experiment demonstrated consistently negative relationships between resident species diversity and community invasibility, irrespective of nitrogen addition, a result further supported by a meta-analysis. Importantly, our experiment showed that plant diversity consistently resisted invasion simultaneously through increased resident biomass, increased trait dissimilarity among residents, and increased community-weighted means of resource-conservative traits that strongly resist invasion, pointing to the importance of both trait complementarity and sampling effects for invasion resistance even under resource enrichment. Our study provides unique evidence that considering species' functional traits can help further our understanding of biotic resistance to biological invasions in a changing environment.
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Affiliation(s)
- Shao-Peng Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.,Institute of Eco-Chongming, Shanghai, China
| | - Pu Jia
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Shu-Ya Fan
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yingtong Wu
- Department of Biology, University of Missouri, St. Louis, Missouri, USA
| | - Xiang Liu
- State Key Laboratory of Grassland Agro-Ecosystems & Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Yani Meng
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yue Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Wen-Sheng Shu
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jin-Tian Li
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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24
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Figueiredo ART, Özkaya Ö, Kümmerli R, Kramer J. Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad. Ecol Lett 2021; 25:138-150. [PMID: 34753204 PMCID: PMC9299690 DOI: 10.1111/ele.13912] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/21/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022]
Abstract
Microbial invasions can compromise ecosystem services and spur dysbiosis and disease in hosts. Nevertheless, the mechanisms determining invasion outcomes often remain unclear. Here, we examine the role of iron‐scavenging siderophores in driving invasions of Pseudomonas aeruginosa into resident communities of environmental pseudomonads. Siderophores can be ‘public goods’ by delivering iron to individuals possessing matching receptors; but they can also be ‘public bads’ by withholding iron from competitors lacking these receptors. Accordingly, siderophores should either promote or impede invasion, depending on their effects on invader and resident growth. Using supernatant feeding and invasion assays, we show that invasion success indeed increased when the invader could use its siderophores to inhibit (public bad) rather than stimulate (public good) resident growth. Conversely, invasion success decreased the more the invader was inhibited by the residents’ siderophores. Our findings identify siderophores as a major driver of invasion dynamics in bacterial communities under iron‐limited conditions.
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Affiliation(s)
- Alexandre R T Figueiredo
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Özhan Özkaya
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Jos Kramer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
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25
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Arnoldi J, Barbier M, Kelly R, Barabás G, Jackson AL. Invasions of ecological communities: Hints of impacts in the invader's growth rate. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Ruth Kelly
- Agri‐Food and Biosciences Institute Belfast UK
| | - György Barabás
- Division of Theoretical Biology Department of IFM Linköping University Linköping Sweden
- ELTE‐MTA Theoretical Biology and Evolutionary Ecology Research Group Budapest Hungary
| | - Andrew L. Jackson
- Zoology Department School of Natural Sciences Trinity College Dublin University of Dublin Dublin Ireland
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26
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Ward CS, Rolison K, Li M, Rozen S, Fisher CL, Lane TW, Thelen MP, Stuart RK. Janthinobacter additions reduce rotifer grazing of microalga Microchloropsis salina in biotically complex communities. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Tan L, Zeng WA, Xiao Y, Li P, Gu S, Wu S, Zhai Z, Feng K, Deng Y, Hu Q. Fungi-Bacteria Associations in Wilt Diseased Rhizosphere and Endosphere by Interdomain Ecological Network Analysis. Front Microbiol 2021; 12:722626. [PMID: 34552573 PMCID: PMC8450586 DOI: 10.3389/fmicb.2021.722626] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
In the plant rhizosphere and endosphere, some fungal and bacterial species regularly co-exist, however, our knowledge about their co-existence patterns is quite limited, especially during invasion by bacterial wilt pathogens. In this study, the fungal communities from soil to endophytic compartments were surveyed during an outbreak of tobacco wilt disease caused by Ralstonia solanacearum. It was found that the stem endophytic fungal community was significantly altered by pathogen invasion in terms of community diversity, structure, and composition. The associations among fungal species in the rhizosphere and endosphere infected by R. solanacearum showed more complex network structures than those of healthy plants. By integrating the bacterial dataset, associations between fungi and bacteria were inferred by Inter-Domain Ecological Network (IDEN) approach. It also revealed that infected samples, including both the rhizosphere and endosphere, had more complex interdomain networks than the corresponding healthy samples. Additionally, the bacterial wilt pathogenic Ralstonia members were identified as the keystone genus within the IDENs of both root and stem endophytic compartments. Ralstonia members was negatively correlated with the fungal genera Phoma, Gibberella, and Alternaria in infected roots, as well as Phoma, Gibberella, and Diaporthe in infected stems. This suggested that those endophytic fungi may play an important role in resisting the invasion of R. solanacearum.
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Affiliation(s)
- Lin Tan
- Hunan Agricultural University, Changsha, China
| | - Wei-Ai Zeng
- Changsha Tobacco Company of Hunan Province, Changsha, China
| | - Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, China
| | - Pengfei Li
- Wenshan Tobacco Company of Yunnan Province, Wenshan, China
| | - Songsong Gu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Institute for Marine Science and Technology, Shandong University, Qingdao, China
| | - Shaolong Wu
- Tobacco Company of Hunan Province, Changsha, China
| | | | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Institute for Marine Science and Technology, Shandong University, Qingdao, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Qiulong Hu
- Hunan Agricultural University, Changsha, China
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28
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Niemeier-Walsh C, Ryan PH, Meller J, Ollberding NJ, Adhikari A, Reponen T. Exposure to traffic-related air pollution and bacterial diversity in the lower respiratory tract of children. PLoS One 2021; 16:e0244341. [PMID: 34166366 PMCID: PMC8224880 DOI: 10.1371/journal.pone.0244341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/26/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Exposure to particulate matter has been shown to increase the adhesion of bacteria to human airway epithelial cells. However, the impact of traffic-related air pollution (TRAP) on the respiratory microbiome is unknown. METHODS Forty children were recruited through the Cincinnati Childhood Allergy and Air Pollution Study, a longitudinal cohort followed from birth through early adolescence. Saliva and induced sputum were collected at age 14 years. Exposure to TRAP was characterized from birth through the time of sample collection using a previously validated land-use regression model. Sequencing of the bacterial 16S and ITS fungal rRNA genes was performed on sputum and saliva samples. The relative abundance of bacterial taxa and diversity indices were compared in children with exposure to high and low TRAP. We also used multiple linear regression to assess the effect of TRAP exposure, gender, asthma status, and socioeconomic status on the alpha diversity of bacteria in sputum. RESULTS We observed higher bacterial alpha diversity indices in sputum than in saliva. The diversity indices for bacteria were greater in the high TRAP exposure group than the low exposure group. These differences remained after adjusting for asthma status, gender, and mother's education. No differences were observed in the fungal microbiome between TRAP exposure groups. CONCLUSION Our findings indicate that exposure to TRAP in early childhood and adolescence may be associated with greater bacterial diversity in the lower respiratory tract. Asthma status does not appear to confound the observed differences in diversity. These results demonstrate that there may be a TRAP-exposure related change in the lower respiratory microbiota that is independent of asthma status.
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Affiliation(s)
- Christine Niemeier-Walsh
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, United States of America
| | - Patrick H. Ryan
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, United States of America
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, United States of America
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
| | - Jaroslaw Meller
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, United States of America
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, United States of America
| | - Nicholas J. Ollberding
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, United States of America
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
| | - Atin Adhikari
- Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, Georgia, United States of America
| | - Tiina Reponen
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, United States of America
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29
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Sierocinski P, Soria Pascual J, Padfield D, Salter M, Buckling A. The impact of propagule pressure on whole community invasions in biomethane-producing communities. iScience 2021; 24:102659. [PMID: 34151242 PMCID: PMC8192723 DOI: 10.1016/j.isci.2021.102659] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/29/2021] [Accepted: 05/25/2021] [Indexed: 01/04/2023] Open
Abstract
Microbes can invade as whole communities, but the ecology of whole community invasions is poorly understood. Here, we investigate how invader propagule pressure (the number of invading organisms) affects the composition and function of invaded laboratory methanogenic communities. An invading community was equally successful at establishing itself in a resident community regardless of propagule pressure, which varied between 0.01 and 10% of the size resident community. Invasion resulted in enhanced biogas production (to the level of the pure invading community) but only when propagule pressure was 1% or greater. This inconsistency between invasion success and changes in function can be explained by a lower richness of invading taxa at lower propagule pressures, and an important functional role of the taxa that were absent. Our results highlight that whole community invasion ecology cannot simply be extrapolated from our understanding of single species invasions. Moreover, we show that methane production can be enhanced by invading poorly performing reactors with a better performing community at levels that may be practical in industrial settings. Complex communities can successfully invade other communities Invasions change the community composition independently of propagule pressure Number of taxa invading increases with increased propagule pressure Larger propagule pressure impacts both the community structure and function
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Affiliation(s)
- Pawel Sierocinski
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| | - Jesica Soria Pascual
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| | - Daniel Padfield
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
| | | | - Angus Buckling
- Environment and Sustainability Institute, Penryn Campus, University of Exeter, Penryn, UK
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30
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VilÀ M, Dunn AM, Essl F, GÓmez-DÍaz E, Hulme PE, Jeschke JM, NÚÑez MA, Ostfeld RS, Pauchard A, Ricciardi A, Gallardo B. Viewing Emerging Human Infectious Epidemics through the Lens of Invasion Biology. Bioscience 2021. [DOI: 10.1093/biosci/biab047] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Invasion biology examines species originated elsewhere and moved with the help of humans, and those species’ impacts on biodiversity, ecosystem services, and human well-being. In a globalized world, the emergence and spread of many human infectious pathogens are quintessential biological invasion events. Some macroscopic invasive species themselves contribute to the emergence and transmission of human infectious agents. We review conceptual parallels and differences between human epidemics and biological invasions by animals and plants. Fundamental concepts in invasion biology regarding the interplay of propagule pressure, species traits, biotic interactions, eco-evolutionary experience, and ecosystem disturbances can help to explain transitions between stages of epidemic spread. As a result, many forecasting and management tools used to address epidemics could be applied to biological invasions and vice versa. Therefore, we advocate for increasing cross-fertilization between the two disciplines to improve prediction, prevention, treatment, and mitigation of invasive species and infectious disease outbreaks, including pandemics.
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Affiliation(s)
- Montserrat VilÀ
- Department of Plant Biology and Ecology, University of Sevilla, Sevilla, Spain
| | | | - Franz Essl
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Elena GÓmez-DÍaz
- Institute of Parasitology and Biomedicine Lopez-Neyra, Granada, Spain
| | - Philip E Hulme
- Bio-Protection Research Centre, Lincoln University, Canterbury, New Zealand
| | - Jonathan M Jeschke
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, with the Institute of Biology, Freie Universität Berlin, and with the Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - MartÍn A NÚÑez
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States
| | - Richard S Ostfeld
- Cary Institute of Ecosystem Studies, Millbrook, New York, United States
| | - AnÍbal Pauchard
- Laboratorio de Invasiones Biológicas, Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, Chile, and with the Institute of Ecology and Biodiversity, Santiago, Chile
| | | | - Belinda Gallardo
- Pyrenean Institute of Ecology, Zaragoza, Spain, and with the BioRISC (Biosecurity Research Initiative at St Catharine's), at St Catharine's College, Cambridge, United Kingdom
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31
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Wei F, Feng H, Zhang D, Feng Z, Zhao L, Zhang Y, Deakin G, Peng J, Zhu H, Xu X. Composition of Rhizosphere Microbial Communities Associated With Healthy and Verticillium Wilt Diseased Cotton Plants. Front Microbiol 2021; 12:618169. [PMID: 33889135 PMCID: PMC8057349 DOI: 10.3389/fmicb.2021.618169] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/22/2021] [Indexed: 01/16/2023] Open
Abstract
Rhizosphere microbial communities are known to be related to plant health; using such an association for crop management requires a better understanding of this relationship. We investigated rhizosphere microbiomes associated with Verticillium wilt symptoms in two cotton cultivars. Microbial communities were profiled by amplicon sequencing, with the total bacterial and fungal DNA quantified by quantitative polymerase chain reaction based on the respective 16S and internal transcribed spacer primers. Although the level of V. dahliae inoculum was higher in the rhizosphere of diseased plants than in the healthy plants, such a difference explained only a small proportion of variation in wilt severities. Compared to healthy plants, the diseased plants had much higher total fungal/bacterial biomass ratio, as represented by quantified total fungal or bacterial DNA. The variability in the fungal/bacterial biomass ratio was much smaller than variability in either fungal or bacterial total biomass among samples within diseased or healthy plants. Diseased plants generally had lower bacterial alpha diversity in their rhizosphere, but such differences in the fungal alpha diversity depended on cultivars. There were large differences in both fungal and bacterial communities between diseased and healthy plants. Many rhizosphere microbial groups differed in their abundance between healthy and diseased plants. There was a decrease in arbuscular mycorrhizal fungi and an increase in several plant pathogen and saprophyte guilds in diseased plants. These findings suggested that V. dahliae infection of roots led to considerable changes in rhizosphere microbial communities, with large increases in saprophytic fungi and reduction in bacterial community.
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Affiliation(s)
- Feng Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China.,State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China
| | - Hongjie Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China.,State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China
| | - Dezheng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zili Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lihong Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yalin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Greg Deakin
- National Institute of Agricultural Botany, East Malling Research, East Malling, United Kingdom
| | - Jun Peng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China.,State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China
| | - Heqin Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China.,State Key Laboratory of Cotton Biology, Zhengzhou Research Base, Zhengzhou University, Zhengzhou, China
| | - Xiangming Xu
- National Institute of Agricultural Botany, East Malling Research, East Malling, United Kingdom
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32
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Boyle JA, Simonsen AK, Frederickson ME, Stinchcombe JR. Priority effects alter interaction outcomes in a legume-rhizobium mutualism. Proc Biol Sci 2021; 288:20202753. [PMID: 33715440 PMCID: PMC7944086 DOI: 10.1098/rspb.2020.2753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Priority effects occur when the order of species arrival affects the final community structure. Mutualists often interact with multiple partners in different orders, but if or how priority effects alter interaction outcomes is an open question. In the field, we paired the legume Medicago lupulina with two nodulating strains of Ensifer bacteria that vary in nitrogen-fixing ability. We inoculated plants with strains in different orders and measured interaction outcomes. The first strain to arrive primarily determined plant performance and final relative abundances of rhizobia on roots. Plants that received effective microbes first and ineffective microbes second grew larger than plants inoculated with the same microbes in the opposite order. Our results show that mutualism outcomes can be influenced not just by partner identity, but by the interaction order. Furthermore, hosts receiving high-quality mutualists early can better tolerate low-quality symbionts later, indicating that priority effects may help explain the persistence of ineffective symbionts.
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Affiliation(s)
- Julia A Boyle
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada M5S3B2
| | - Anna K Simonsen
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia.,Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada M5S3B2
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada M5S3B2.,Koffler Scientific Reserve, University of Toronto, Toronto, Ontario, Canada M5S3B2
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33
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Wang NR, Wiesmann CL, Melnyk RA, Hossain SS, Chi MH, Martens K, Craven K, Haney CH. Commensal Pseudomonas fluorescens Strains Protect Arabidopsis from Closely Related Pseudomonas Pathogens in a Colonization-Dependent Manner. mBio 2021; 13:e0289221. [PMID: 35100865 PMCID: PMC8805031 DOI: 10.1128/mbio.02892-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022] Open
Abstract
Plants form commensal associations with soil microorganisms, creating a root microbiome that provides benefits, including protection against pathogens. While bacteria can inhibit pathogens through the production of antimicrobial compounds in vitro, it is largely unknown how microbiota contribute to pathogen protection in planta. We developed a gnotobiotic model consisting of Arabidopsis thaliana and the opportunistic pathogen Pseudomonas sp. N2C3, to identify mechanisms that determine the outcome of plant-pathogen-microbiome interactions in the rhizosphere. We screened 25 phylogenetically diverse Pseudomonas strains for their ability to protect against N2C3 and found that commensal strains closely related to N2C3, including Pseudomonas sp. WCS365, were more likely to protect against pathogenesis. We used comparative genomics to identify genes unique to the protective strains and found no genes that correlate with protection, suggesting that variable regulation of components of the core Pseudomonas genome may contribute to pathogen protection. We found that commensal colonization level was highly predictive of protection, so we tested deletions in genes required for Arabidopsis rhizosphere colonization. We identified a response regulator colR, and two ColR-dependent genes with predicted roles in membrane modifications (warB and pap2_2), that are required for Pseudomonas-mediated protection from N2C3. We found that WCS365 also protects against the agricultural pathogen Pseudomonas fuscovaginae SE-1, the causal agent of bacterial sheath brown rot of rice, in a ColR-dependent manner. This work establishes a gnotobiotic model to uncover mechanisms by which members of the microbiome can protect hosts from pathogens and informs our understanding of the use of beneficial strains for microbiome engineering in dysbiotic soil systems. IMPORTANCE Microbiota can protect diverse hosts from pathogens, and microbiome dysbiosis can result in increased vulnerability to opportunistic pathogens. Here, we developed a rhizosphere commensal-pathogen model to identify bacterial strains and mechanisms that can protect plants from an opportunistic Pseudomonas pathogen. Our finding that protective strains are closely related to the pathogen suggests that the presence of specific microbial taxa may help protect plants from disease. We found that commensal colonization level was highly correlated with protection, suggesting that competition with pathogens may play a role in protection. As we found that commensal Pseudomonas were also able to protect against an agricultural pathogen, this system may be broadly relevant for identifying strains and mechanisms to control agriculturally important pathogens. This work also suggests that beneficial plant-associated microbes may be useful for engineering soils where microbial complexity is low, such as hydroponic, or disturbed agricultural soils.
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Affiliation(s)
- Nicole R. Wang
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Christina L. Wiesmann
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan A. Melnyk
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarzana S. Hossain
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Kitoosepe Martens
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kelly Craven
- Noble Research Institute, Ardmore, Oklahoma, USA
| | - Cara H. Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
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34
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Mitter EK, Tosi M, Obregón D, Dunfield KE, Germida JJ. Rethinking Crop Nutrition in Times of Modern Microbiology: Innovative Biofertilizer Technologies. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.606815] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Global population growth poses a threat to food security in an era of increased ecosystem degradation, climate change, soil erosion, and biodiversity loss. In this context, harnessing naturally-occurring processes such as those provided by soil and plant-associated microorganisms presents a promising strategy to reduce dependency on agrochemicals. Biofertilizers are living microbes that enhance plant nutrition by either by mobilizing or increasing nutrient availability in soils. Various microbial taxa including beneficial bacteria and fungi are currently used as biofertilizers, as they successfully colonize the rhizosphere, rhizoplane or root interior. Despite their great potential to improve soil fertility, biofertilizers have yet to replace conventional chemical fertilizers in commercial agriculture. In the last 10 years, multi-omics studies have made a significant step forward in understanding the drivers, roles, processes, and mechanisms in the plant microbiome. However, translating this knowledge on microbiome functions in order to capitalize on plant nutrition in agroecosystems still remains a challenge. Here, we address the key factors limiting successful field applications of biofertilizers and suggest potential solutions based on emerging strategies for product development. Finally, we discuss the importance of biosafety guidelines and propose new avenues of research for biofertilizer development.
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35
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Jones ML, Rivett DW, Pascual-García A, Bell T. Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms. eLife 2021; 10:71811. [PMID: 34662276 PMCID: PMC8523168 DOI: 10.7554/elife.71811] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/19/2021] [Indexed: 01/03/2023] Open
Abstract
Common garden experiments that inoculate a standardised growth medium with synthetic microbial communities (i.e. constructed from individual isolates or using dilution cultures) suggest that the ability of the community to resist invasions by additional microbial taxa can be predicted by the overall community productivity (broadly defined as cumulative cell density and/or growth rate). However, to the best of our knowledge, no common garden study has yet investigated the relationship between microbial community composition and invasion resistance in microcosms whose compositional differences reflect natural, rather than laboratory-designed, variation. We conducted experimental invasions of two bacterial strains (Pseudomonas fluorescens and Pseudomonas putida) into laboratory microcosms inoculated with 680 different mixtures of bacteria derived from naturally occurring microbial communities collected in the field. Using 16S rRNA gene amplicon sequencing to characterise microcosm starting composition, and high-throughput assays of community phenotypes including productivity and invader survival, we determined that productivity is a key predictor of invasion resistance in natural microbial communities, substantially mediating the effect of composition on invasion resistance. The results suggest that similar general principles govern invasion in artificial and natural communities, and that factors affecting resident community productivity should be a focal point for future microbial invasion experiments.
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Affiliation(s)
- Matt Lloyd Jones
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscotUnited Kingdom
| | - Damian William Rivett
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscotUnited Kingdom
| | - Alberto Pascual-García
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscotUnited Kingdom
| | - Thomas Bell
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscotUnited Kingdom
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36
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Heyse J, Props R, Kongnuan P, De Schryver P, Rombaut G, Defoirdt T, Boon N. Rearing water microbiomes in white leg shrimp (Litopenaeus vannamei) larviculture assemble stochastically and are influenced by the microbiomes of live feed products. Environ Microbiol 2020; 23:281-298. [PMID: 33169932 DOI: 10.1111/1462-2920.15310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/21/2020] [Accepted: 11/06/2020] [Indexed: 01/22/2023]
Abstract
The development of effective management strategies to reduce the occurrence of diseases in aquaculture is hampered by the limited knowledge on the microbial ecology of these systems. In this study, the dynamics and dominant community assembly processes in the rearing water of Litopenaeus vannamei larviculture tanks were determined. Additionally, the contribution of peripheral microbiomes, such as those of live and dry feeds, to the rearing water microbiome were quantified. The community assembly in the hatchery rearing water over time was dominated by stochasticity, which explains the observed heterogeneity between replicate cultivations. The community undergoes two shifts that match with the dynamics of the algal abundances in the rearing water. Source tracking analysis revealed that 37% of all bacteria in the hatchery rearing water were introduced either by the live or dry feeds, or during water exchanges. The contribution of the microbiome from the algae was the largest, followed by that of the Artemia, the exchange water and the dry feeds. Our findings provide fundamental knowledge on the assembly processes and dynamics of rearing water microbiomes and illustrate the crucial role of these peripheral microbiomes in maintaining health-promoting rearing water microbiomes.
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Affiliation(s)
- Jasmine Heyse
- Center for Microbial Ecology and Technology (CMET), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Ruben Props
- Center for Microbial Ecology and Technology (CMET), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | | | | | - Geert Rombaut
- INVE Technologies NV, Hoogveld 93, Dendermonde, 9200, Belgium
| | - Tom Defoirdt
- Center for Microbial Ecology and Technology (CMET), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
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37
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van der Goot E, van Spronsen FJ, Falcão Salles J, van der Zee EA. A Microbial Community Ecology Perspective on the Gut-Microbiome-Brain Axis. Front Endocrinol (Lausanne) 2020; 11:611. [PMID: 32982988 PMCID: PMC7492586 DOI: 10.3389/fendo.2020.00611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Els van der Goot
- Molecular Neurobiology, Groningen Institute for Evolutionary Sciences, University of Groningen, Groningen, Netherlands
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Sciences, University of Groningen, Groningen, Netherlands
| | - Francjan J. van Spronsen
- Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, Netherlands
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Sciences, University of Groningen, Groningen, Netherlands
| | - Eddy A. van der Zee
- Molecular Neurobiology, Groningen Institute for Evolutionary Sciences, University of Groningen, Groningen, Netherlands
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Augelletti F, Jousset A, Agathos SN, Stenuit B. Diversity Manipulation of Psychrophilic Bacterial Consortia for Improved Biological Treatment of Medium-Strength Wastewater at Low Temperature. Front Microbiol 2020; 11:1490. [PMID: 32793129 PMCID: PMC7393979 DOI: 10.3389/fmicb.2020.01490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/08/2020] [Indexed: 11/13/2022] Open
Abstract
Psychrophilic bacteria are valuable biocatalysts to develop robust bioaugmentation formulations for enhanced wastewater treatment at low temperatures or fluctuating temperature conditions. Here, using different biodiversity indices [based on species richness (SR), phylogenetic diversity (PD) and functional diversity (FD)], we studied the effects of microbial diversity of artificial bacterial consortia on the biomass gross yields (measured through OD600) and removal efficiency of soluble chemical oxygen demand (mg sCOD removed/mg sCOD introduced) in synthetic, medium-strength wastewater. We built artificial consortia out of one to six bacterial strains isolated at 4°C through combinatorial biodiversity experiments. Increasing species richness resulted in improved sCOD removal efficiency (i.e., 0.266 ± 0.146, 0.542 ± 0.155, 0.742 ± 0.136, 0.822 ± 0.019 for mono-, tri-, penta-and hexacultures, respectively) and higher biomass gross yields (i.e., 0.065 ± 0.052, 0.132 ± 0.046, 0.173 ± 0.049, 0.216 ± 0.019 for mono-, tri-, penta,- and hexacultures, respectively). This positive relationship between biodiversity, sCOD removal and biomass gross yield was also observed when considering metabolic profiling (functional diversity) or evolutionary relationships (phylogenetic diversity). The positive effect of biodiversity on sCOD removal efficiency could be attributed to the selection of a particular, best-performing species (i.e., Pedobacter sp.) as well as complementary use of carbon resources among consortia members (i.e., complementarity effects). Among the biodiversity indices, PD diversity metrics explained higher variation in sCOD removal than SR and FD diversity metrics. For a more effective bioaugmentation, our results stress the importance of using phylogenetically diverse consortia, with an increased degradation ability, instead of single pure cultures. Moreover, PD could be used as an assembly rule to guide the composition of mixed cultures for wastewater bioaugmentation under psychrophilic conditions.
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Affiliation(s)
- Floriana Augelletti
- Laboratory of Bioengineering, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
| | - Alexandre Jousset
- Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Spiros N Agathos
- Laboratory of Bioengineering, Earth and Life Institute, Catholic University of Louvain, Louvain-la-Neuve, Belgium
| | - Benoit Stenuit
- Joint Research Unit of Agropolymer Engineering and Emerging Technologies (IATE, UMR 1208), Polytech Montpellier, University of Montpellier, Montpellier, France
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Cleary DFR, Polónia ARM, Reijnen BT, Berumen ML, de Voogd NJ. Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea. MICROBIAL ECOLOGY 2020; 80:103-119. [PMID: 31932882 DOI: 10.1007/s00248-019-01465-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.
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Affiliation(s)
- D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - A R M Polónia
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - B T Reijnen
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - M L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - N J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Environmental Sciences, Environmental Biology Department, Leiden University, Leiden, The Netherlands
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40
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Carvalho CR, Dias AC, Homma SK, Cardoso EJ. Phyllosphere bacterial assembly in citrus crop under conventional and ecological management. PeerJ 2020; 8:e9152. [PMID: 32547860 PMCID: PMC7274167 DOI: 10.7717/peerj.9152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/17/2020] [Indexed: 11/20/2022] Open
Abstract
Divergences between agricultural management can result in different types of biological interactions between plants and microorganisms, which may affect food quality and productivity. Conventional practices are well-established in the agroindustry as very efficient and lucrative; however, the increasing demand for sustainable alternatives has turned attention towards agroecological approaches. Here we intend to explore microbial dynamics according to the agricultural management used, based on the composition and structure of these bacterial communities on the most environmentally exposed habitat, the phyllosphere. Leaf samples were collected from a Citrus crop (cultivated Orange) in Mogi-Guaçu (SP, Brazil), where either conventional or ecological management systems were properly applied in two different areas. NGS sequencing analysis and quantitative PCR allowed us to comprehend the phyllosphere behavior and µ-XRF (micro X-ray fluorescence) could provide an insight on agrochemical persistence on foliar tissues. Our results demonstrate that there is considerable variation in the phyllosphere community due to the management practices used in the citrus orchard, and it was possible to quantify most of this variation. Equally, high copper concentrations may have influenced bacterial abundance, having a relevant impact on the differences observed. Moreover, we highlight the intricate relationship microorganisms have with crop production, and presumably with crop yield as well.
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Affiliation(s)
- Carolinne R Carvalho
- Department of Soil Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Armando Cf Dias
- Department of Soil Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Elke Jbn Cardoso
- Department of Soil Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, São Paulo, Brazil
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Eckert EM, Quero GM, Di Cesare A, Manfredini G, Mapelli F, Borin S, Fontaneto D, Luna GM, Corno G. Antibiotic disturbance affects aquatic microbial community composition and food web interactions but not community resilience. Mol Ecol 2019; 28:1170-1182. [PMID: 30697889 DOI: 10.1111/mec.15033] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/13/2018] [Accepted: 01/14/2019] [Indexed: 01/17/2023]
Abstract
Notwithstanding the fundamental role that environmental microbes play for ecosystem functioning, data on how microbes react to disturbances are still scarce, and most factors that confer stability to microbial communities are unknown. In this context, antibiotic discharge into the environment is considered a worldwide threat for ecosystems with potential risks to human health. We therefore tested resilience of microbial communities challenged by the presence of an antibiotic. In a continuous culture experiment, we compared the abundance, composition and diversity of microbial communities undisturbed or disturbed by the constant addiction of tetracycline in low (10 µg/L) or intermediate (100 µg/L) concentration (press disturbance). Further, the bacterial communities in the three treatments had to face the sudden pulse disturbance of adding an allochthonous bacterium (Escherichia coli). Tetracycline, even at low concentrations, affected microbial communities by changing their phylogenetic composition and causing cell aggregation. This, however, did not coincide with a reduced microbial diversity, but was mainly caused by a shift in dominance of specific bacterial families. Moreover, the less disturbed community (10 µg/L tetracycline) was sometimes more similar to the control and sometimes more similar to heavily disturbed community (100 µg/L tetracycline). All in all, we could not see a pattern where the communities disturbed with antibiotics were less resilient to a second disturbance introducing E. coli, but they seemed to be able to buffer the input of the allochthonous strain in a similar manner as the control.
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Affiliation(s)
- Ester M Eckert
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Grazia M Quero
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn (SZN), Napoli, Italy
| | - Andrea Di Cesare
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy.,Department of Environmental and Life Sciences (DISTAV), University of Genoa, Genova, Italy
| | - Giuliana Manfredini
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milano, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milano, Italy
| | - Diego Fontaneto
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
| | - Gian Marco Luna
- National Research Council, Istituto per le Risorse Biologiche e le Biotecnologie Marine (CNR-IRBIM), Ancona, Italy
| | - Gianluca Corno
- Microbial Ecology Group, National Research Council - Water Research Institute (CNR-IRSA), Verbania, Italy
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Saleem M, Hu J, Jousset A. More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110617-062605] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microorganisms drive several processes needed for robust plant growth and health. Harnessing microbial functions is thus key to productive and sustainable food production. Molecular methods have led to a greater understanding of the soil microbiome composition. However, translating species or gene composition into microbiome functionality remains a challenge. Community ecology concepts such as the biodiversity–ecosystem functioning framework may help predict the assembly and function of plant-associated soil microbiomes. Higher diversity can increase the number and resilience of plant-beneficial functions that can be coexpressed and unlock the expression of plant-beneficial traits that are hard to obtain from any species in isolation. We combine well-established community ecology concepts with molecular microbiology into a workable framework that may enable us to predict and enhance soil microbiome functionality to promote robust plant growth in a global change context.
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Affiliation(s)
- Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, Alabama 36104, USA
| | - Jie Hu
- Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Alexandre Jousset
- Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, 3584 CH Utrecht, The Netherlands
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43
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Margos G, Fingerle V, Reynolds S. Borrelia bavariensis: Vector Switch, Niche Invasion, and Geographical Spread of a Tick-Borne Bacterial Parasite. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00401] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Thakur MP, van der Putten WH, Cobben MMP, van Kleunen M, Geisen S. Microbial invasions in terrestrial ecosystems. Nat Rev Microbiol 2019; 17:621-631. [DOI: 10.1038/s41579-019-0236-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2019] [Indexed: 01/08/2023]
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Darlison J, Mogren L, Rosberg AK, Grudén M, Minet A, Liné C, Mieli M, Bengtsson T, Håkansson Å, Uhlig E, Becher PG, Karlsson M, Alsanius BW. Leaf mineral content govern microbial community structure in the phyllosphere of spinach (Spinacia oleracea) and rocket (Diplotaxis tenuifolia). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 675:501-512. [PMID: 31030156 DOI: 10.1016/j.scitotenv.2019.04.254] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
The plant microbiome is an important factor for plant health and productivity. While the impact of nitrogen (N) availability for plant growth and development is well established, its influence on the microbial phyllosphere community structure is unknown. We hypothesize that nitrogen impacts the growth and abundance of several microorganisms on the leaf surface. The bacterial and fungal communities of baby leaf spinach (Spinacia oleracea), and rocket (Diplotaxis tenuifolia) were investigated in a field trial for two years in a commercial setting. Nitrogen fertilizer was tested in four doses (basic nitrogen, basic + suboptimal, basic + commercial, basic + excess) with six replicates in each. Culture-independent (Illumina sequencing) and culture-dependent (viable count and identification of bacterial isolates) community studies were combined with monitoring of plant physiology and site weather conditions. This study found that alpha diversity of bacterial communities decreased in response to increasing nitrogen fertilizer dose, whereas viable counts showed no differences. Correspondingly, fungal communities of the spinach phyllosphere showed a decreasing pattern, whereas the decreasing diversity of fungal communities of rocket was not significant. Plant species and effects of annual variations on microbiome structure were observed for bacterial and fungal communities on both spinach and rocket. This study provides novel insights on the impact of nitrogen fertilizer regime on a nutrient scarce habitat, the phyllosphere.
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Affiliation(s)
- Julia Darlison
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden.
| | - Lars Mogren
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Anna Karin Rosberg
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Maria Grudén
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Antoine Minet
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Clarisse Liné
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Morgane Mieli
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Torbjörn Bengtsson
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Åsa Håkansson
- LTH Lund University, Department of Food Technology, Box 124, SE-221 00 Lund, Sweden
| | - Elisabeth Uhlig
- LTH Lund University, Department of Food Technology, Box 124, SE-221 00 Lund, Sweden
| | - Paul G Becher
- Swedish University of Agricultural Sciences, Department of Plant Protection Biology, PO Box 102, SE-230 53 Alnarp, Sweden
| | - Maria Karlsson
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Beatrix W Alsanius
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
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Li SP, Tan J, Yang X, Ma C, Jiang L. Niche and fitness differences determine invasion success and impact in laboratory bacterial communities. THE ISME JOURNAL 2019; 13:402-412. [PMID: 30254322 PMCID: PMC6331569 DOI: 10.1038/s41396-018-0283-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 08/28/2018] [Accepted: 09/08/2018] [Indexed: 11/09/2022]
Abstract
There is increasing awareness of invasion in microbial communities worldwide, but the mechanisms behind microbial invasions remain poorly understood. Specifically, we know little about how the evolutionary and ecological differences between invaders and natives regulate invasion success and impact. Darwin's naturalization hypothesis suggests that the phylogenetic distance between invaders and natives could be a useful predictor of invasion, and modern coexistence theory proposes that invader-native niche and fitness differences combine to determine invasion outcome. However, the relative importance of phylogenetic distance, niche difference and fitness difference for microbial invasions has rarely been examined. By using laboratory bacterial microcosms as model systems, we experimentally assessed the roles of these differences for the success of bacterial invaders and their impact on native bacterial community structure. We found that the phylogenetic distance between invaders and natives failed to explain invasion success and impact for two of three invaders at the phylogenetic scale considered. Further, we found that invasion success was better explained by invader-native niche differences than relative fitness differences for all three invaders, whereas invasion impact was better explained by invader-native relative fitness differences than niche differences. These findings highlight the utility of considering modern coexistence theory to gain a more mechanistic understanding of microbial invasions.
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Affiliation(s)
- Shao-Peng Li
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jiaqi Tan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Xian Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Chao Ma
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, 230036, Hefei, Anhui, China.
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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Invasion triple trouble: environmental fluctuations, fluctuation-adapted invaders and fluctuation-mal-adapted communities all govern invasion success. BMC Evol Biol 2019; 19:42. [PMID: 30709335 PMCID: PMC6359858 DOI: 10.1186/s12862-019-1348-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 01/02/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It has been suggested that climate change will lead to increased environmental fluctuations, which will undoubtedly have evolutionary consequences for all biota. For instance, fluctuations can directly increase the risk of invasions of alien species into new areas, as these species have repeatedly been proposed to benefit from disturbances. At the same time increased environmental fluctuations may also select for better invaders. However, selection by fluctuations may also influence the resistance of communities to invasions, which has rarely been tested. We tested eco-evolutionary dynamics of invasion with bacterial clones, evolved either in constant or fluctuating temperatures, and conducted experimental invasions in both conditions. RESULTS We found clear evidence that ecological fluctuations, as well as adaptation to fluctuations by both the invader and community, all affected invasions, but played different roles at different stages of invasion. Ecological fluctuations clearly promoted invasions, especially into fluctuation mal-adapted communities. The evolutionary background of the invader played a smaller role. CONCLUSIONS Our results indicate that climate change associated disturbances can directly increase the risk of invasions by altering ecological conditions during invasions, as well as via the evolution of both the invader and communities. Our experiment provides novel information on the complex consequences of climate change on invasions in general, and also charts risk factors associated with the spread of environmentally growing opportunistic pathogens.
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48
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Shi W, Li M, Wei G, Tian R, Li C, Wang B, Lin R, Shi C, Chi X, Zhou B, Gao Z. The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome. MICROBIOME 2019; 7:14. [PMID: 30709420 PMCID: PMC6359780 DOI: 10.1186/s40168-019-0629-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 01/17/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulosphere soil (GS), rhizosphere soil (RS), root-zone soil (ZS), and furrow soil (FS)) were analyzed for potato plants with naturally high (H) and low (L) scab severity levels. We aimed to determine the composition and putative function of the soil microbiome associated with potato CS. RESULTS The copy numbers of the scab phytotoxin biosynthetic gene txtAB and the bacterial 16S rRNA gene as well as the diversity and composition of each of the four soil-root system compartments were examined; GS was the only compartment that exhibited significant differences between the H and L groups. Compared to the H group, the L group exhibited a lower txtAB gene copy number, lower bacterial 16S copy number, higher diversity, higher co-occurrence network complexity, and higher community function similarity within the GS microbiome. The community composition and function of the GS samples were further revealed by shotgun metagenomic sequencing. Variovorax, Stenotrophomonas, and Agrobacterium were the most abundant genera that were significantly and positively correlated with the scab severity level, estimated absolute abundance (EAA) of pathogenic Streptomyces, and txtAB gene copy number. In contrast, Geobacillus, Curtobacterium, and unclassified Geodermatophilaceae were significantly negatively correlated with these three parameters. Compared to the function profiles in the L group, several genes involved in "ABC transporters," the "bacterial secretion system," "quorum sensing (QS)," "nitrogen metabolism," and some metabolism by cytochrome P450 were enriched in the H group. In contrast, some antibiotic biosynthesis pathways were enriched in the L group. Based on the differences in community composition and function, a simple model was proposed to explain the putative relationships between the soil microbiome and CS occurrence. CONCLUSIONS The GS microbiome was closely associated with CS severity in the soil-root system, and the occurrence of CS was accompanied by changes in community composition and function. The differential functions provide new clues to elucidate the mechanism underlying the interaction between CS occurrence and the soil microbiome, and varying community compositions provide novel insights into CS occurrence.
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Affiliation(s)
- Wencong Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Mingcong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Guangshan Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, 361005, China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-Sen University, Guangzhou, 510275, China
| | - Renmao Tian
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, USA
| | - Cuiping Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Bing Wang
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China
| | - Rongshan Lin
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China
| | - Chunyu Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiuli Chi
- Plant Protection Station, Jiaozhou Agricultural Bureau, Qingdao, 266300, China
| | - Bo Zhou
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China.
| | - Zheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China.
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, USA.
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49
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Assessing the resilience of biodiversity-driven functions in agroecosystems under environmental change. ADV ECOL RES 2019. [DOI: 10.1016/bs.aecr.2019.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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50
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Yang T, Han G, Yang Q, Friman VP, Gu S, Wei Z, Kowalchuk GA, Xu Y, Shen Q, Jousset A. Resource stoichiometry shapes community invasion resistance via productivity-mediated species identity effects. Proc Biol Sci 2018; 285:20182035. [PMID: 30963908 PMCID: PMC6304049 DOI: 10.1098/rspb.2018.2035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/17/2018] [Indexed: 11/12/2022] Open
Abstract
Diversity-invasion resistance relationships are often variable and sensitive to environmental conditions such as resource availability. Resource stoichiometry, the relative concentration of different elements in the environment, has been shown to have strong effects on the physiology and interactions between different species. Yet, its role for diversity-invasion resistance relationships is still poorly understood. Here, we explored how the ratio of nitrogen (N) and phosphorus affects the productivity and invasion resistance of constructed microbial communities by a plant pathogenic bacterium, Ralstonia solanacearum. We found that resource stoichiometry and species identity effects affected the invasion resistance of communities. Both high N concentration and resident community diversity constrained invasions, and two resident species, in particular, had strong negative effects on the relative density of the invader and the resident community productivity. While resource stoichiometry did not affect the mean productivity of the resident community, it favoured the growth of two species that strongly constrained invasions turning the slope of productivity-invasion resistance relationship more negative. Together our findings suggest that alterations in resource stoichiometry can change the community resistance to invasions by having disproportionate effects on species growth, potentially explaining changes in microbial community composition under eutrophication.
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Affiliation(s)
- Tianjie Yang
- Jiangsu Provincial Key Lab 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, People's Republic of China
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Gang Han
- Jiangsu Provincial Key Lab 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, People's Republic of China
| | - Qingjun Yang
- Jiangsu Provincial Key Lab 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, People's Republic of China
| | - Ville-Petri Friman
- Jiangsu Provincial Key Lab 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, People's Republic of China
- Department of Biology, University of York, Wentworth Way, YO10 5DD, York, UK
| | - Shaohua Gu
- Jiangsu Provincial Key Lab 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, People's Republic of China
| | - Zhong Wei
- Jiangsu Provincial Key Lab 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, People's Republic of China
| | - George A. Kowalchuk
- Jiangsu Provincial Key Lab 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, People's Republic of China
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Yangchun Xu
- Jiangsu Provincial Key Lab 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, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab 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, People's Republic of China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab 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, People's Republic of China
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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