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do Carmo KB, Dias R, de Quadros PD, Berber GCM, Bourscheidt MLB, de Farias Neto AL, Dos Santos Weber OL, Triplett EW, Ferreira A. Assessment of soil bacterial communities in integrated crop production systems within the Amazon Biome, Brazil: a comparative study. Braz J Microbiol 2024; 55:2815-2825. [PMID: 38696039 PMCID: PMC11405747 DOI: 10.1007/s42770-024-01352-8] [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: 10/25/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Integrated production systems have been proposed as alternative to sustainable land use. However, information regarding bacterial community structure and diversity in soils of integrated Crop-Livestock-Forest systems remains unknown. We hypothesize that these integrated production systems, with their ecological intensification, can modulate the soil bacterial communities. However, Yet, it remains unclear whether the modulation of bacterial biodiversity is solely attributable to the complexity of root exudates or if seasonal climatic events also play a contributory role. The objective of this study is to evaluate the impact of monoculture and integrated production systems on bacterial soil communities in the Amazon Biome, Brazil. Three monoculture systems, each with a single crop over time and space (Eucalyptus (E), Crop Soybean (C), Pasture (P)), and three integrated systems with multiple crops over time and space (ECI, PI, ECPI) were evaluated, along with a Native forest serving as a reference area. Soil samples were collected at a depth of 0-10 cm during both the wet and dry seasons. Bacterial composition was determined using Illumina high-throughput sequencing of the 16 S rRNA gene. The sequencing results revealed the highest abundance classified under the phyla Firmicutes, Actinobacteria, and Proteobacteria. The Firmicutes correlated with the Crop in the rainy period and in the dry only ECPI and Forest. For five classes corresponding to the three phyla, the Crop stood out with the greatest fluctuations in their relative abundance compared to other production systems. In cluster analysis by genus during the rainy season, only Forest and ECPI showed no similarity with the other production systems. However, in the dry season, both were grouped with Forest and EPI. Therefore, the bacterial community in integrated systems proved to be sensitive to management practices, even with only two years of use. ECPI demonstrated the greatest similarity in bacterial structure to the Native forest, despite just two years of experimental deployment. Crop exhibited fluctuations in relative abundance in both seasons, indicating an unsustainable production system with changes in soil microbial composition. These findings support our hypothesis that integrated production systems and their ecological intensification, as exemplified by ECPI, can indeed modulate soil bacterial communities.
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Affiliation(s)
- Kellen Banhos do Carmo
- Programa de pós graduação em Agricultura Tropical, Universidade Federal de Mato Grosso (UFMT), Campus Central, Cuiabá, MT, 78060-900, Brazil
| | - Raquel Dias
- Microbiology & Cell Science Department, University of Florida (UF), Gainesville, FL, 110-700, USA
| | - Patricia Dorr de Quadros
- Departamento de Solos e Bioquímica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90410-000, Brazil
| | - Gilcele Campos Martin Berber
- Programa de pós graduação em Ciências Ambientais, Universidade Federal de Mato Grosso (UFMT), Campus Sinop, Sinop, MT, 78550-000, Brazil
| | - Maira Laís Both Bourscheidt
- Curso de graduação em Zootecnia, Universidade Federal de Mato Grosso (UFMT), Campus Sinop, Sinop, MT, 78550-000, Brazil
| | - Austeclinio Lopes de Farias Neto
- Embrapa Agrossilvipastoril - Empresa Brasileira de Pesquisa Agropecuária; endereço atual Embrapa Trigo, Passo Fundo, RS, 99050-970, Brazil
| | - Oscarlina Lucia Dos Santos Weber
- Programa de pós graduação em Agricultura Tropical, Universidade Federal de Mato Grosso (UFMT), Campus Central, Cuiabá, MT, 78060-900, Brazil
| | - Eric W Triplett
- Microbiology & Cell Science Department, University of Florida (UF), Gainesville, FL, 110-700, USA
| | - Anderson Ferreira
- Programa de pós graduação em Agricultura Tropical, Universidade Federal de Mato Grosso (UFMT), Campus Central, Cuiabá, MT, 78060-900, Brazil.
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Lu C, Xiao Z, Li H, Han R, Sun A, Xiang Q, Zhu Z, Li G, Yang X, Zhu YG, Chen QL. Aboveground plants determine the exchange of pathogens within air-phyllosphere-soil continuum in urban greenspaces. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133149. [PMID: 38056267 DOI: 10.1016/j.jhazmat.2023.133149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
The microbiome in the air-phyllosphere-soil continuum of urban greenspaces plays a crucial role in re-connecting urban populations with biodiverse environmental microbiomes. However, little is known about whether plant type affects the airborne microbiomes, as well as the extent to which soil and phyllosphere microbiomes contribute to airborne microbiomes. Here we collected soil, phyllosphere and airborne microbes with different plant types (broadleaf tree, conifer tree, and grass) in urban parks. Despite the significant impacts of plant type on soil and phyllosphere microbiomes, plant type had no obvious effects on the diversity of airborne microbes but shaped airborne bacterial composition in urban greenspaces. Soil and phyllosphere microbiomes had a higher contribution to airborne bacteria in broadleaf trees (37.56%) compared to conifer trees (9.51%) and grasses (14.29%). Grass areas in urban greenspaces exhibited a greater proportion of potential pathogens compared to the tree areas. The abundance of bacterial pathogens in phyllosphere was significantly higher in grasses compared to broadleaf and conifer trees. Together, our study provides novel insights into the microbiome patterns in air-phyllosphere-soil continuum, highlighting the potential significance of reducing the proportion of extensively human-intervened grass areas in future urban environment designs to enhance the provision of ecosystem services in urban greenspaces.
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Affiliation(s)
- Changyi Lu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Zufei Xiao
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruixia Han
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Qian Xiang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Zhe Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham, Ningbo 315100, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Hudson JE, Levia DF, Yoshimura KM, Gottel NR, Hudson SA, Biddle JF. Mapping bark bacteria: initial insights of stemflow-induced changes in bark surface phyla. Microbiol Spectr 2023; 11:e0356223. [PMID: 37971233 PMCID: PMC10715197 DOI: 10.1128/spectrum.03562-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Compared with the phyllosphere, bacteria inhabiting bark surfaces are inadequately understood. Based on a preliminary pilot study, our work suggests that microbial populations vary across tree bark surfaces and may differ in relation to surrounding land use. Initial results suggest that stemflow, the water that flows along the bark surface, actively moves bacterial communities across a tree. These preliminary findings underscore the need for further study of niche microbial populations to determine whether there are connections between the biodiversity of microbiomes inhabiting corticular surfaces, land use, and hydrology.
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Affiliation(s)
- J. E. Hudson
- Department of Geography and Spatial Sciences, University of Delaware, Newark, Delaware, USA
| | - D. F. Levia
- Department of Geography and Spatial Sciences, University of Delaware, Newark, Delaware, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
| | - K. M. Yoshimura
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
| | - N. R. Gottel
- Argonne National Lab, University of Chicago Medicine, Chicago, Illinois, USA
| | - S. A. Hudson
- Department of Geography and Spatial Sciences, University of Delaware, Newark, Delaware, USA
| | - J. F. Biddle
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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Hakobyan A, Velte S, Sickel W, Quandt D, Stoll A, Knief C. Tillandsia landbeckii phyllosphere and laimosphere as refugia for bacterial life in a hyperarid desert environment. MICROBIOME 2023; 11:246. [PMID: 37936139 PMCID: PMC10631034 DOI: 10.1186/s40168-023-01684-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/28/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND The lack of water is a major constraint for microbial life in hyperarid deserts. Consequently, the abundance and diversity of microorganisms in common habitats such as soil are strongly reduced, and colonization occurs primarily by specifically adapted microorganisms that thrive in particular refugia to escape the harsh conditions that prevail in these deserts. We suggest that plants provide another refugium for microbial life in hyperarid deserts. We studied the bacterial colonization of Tillandsia landbeckii (Bromeliaceae) plants, which occur in the hyperarid regions of the Atacama Desert in Chile, one of the driest and oldest deserts on Earth. RESULTS We detected clear differences between the bacterial communities being plant associated to those of the bare soil surface (PERMANOVA, R2 = 0.187, p = 0.001), indicating that Tillandsia plants host a specific bacterial community, not only dust-deposited cells. Moreover, the bacterial communities in the phyllosphere were distinct from those in the laimosphere, i.e., on buried shoots (R2 = 0.108, p = 0.001), indicating further habitat differentiation within plant individuals. The bacterial taxa detected in the phyllosphere are partly well-known phyllosphere colonizers, but in addition, some rather unusual taxa (subgroup2 Acidobacteriae, Acidiphilum) and insect endosymbionts (Wolbachia, "Candidatus Uzinura") were found. The laimosphere hosted phyllosphere-associated as well as soil-derived taxa. The phyllosphere bacterial communities showed biogeographic patterns across the desert (R2 = 0.331, p = 0.001). These patterns were different and even more pronounced in the laimosphere (R2 = 0.467, p = 0.001), indicating that different factors determine community assembly in the two plant compartments. Furthermore, the phyllosphere microbiota underwent temporal changes (R2 = 0.064, p = 0.001). CONCLUSIONS Our data demonstrate that T. landbeckii plants host specific bacterial communities in the phyllosphere as well as in the laimosphere. Therewith, these plants provide compartment-specific refugia for microbial life in hyperarid desert environments. The bacterial communities show biogeographic patterns and temporal variation, as known from other plant microbiomes, demonstrating environmental responsiveness and suggesting that bacteria inhabit these plants as viable microorganisms. Video Abstract.
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Affiliation(s)
- Anna Hakobyan
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Stefanie Velte
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Wiebke Sickel
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
- Institute of Biodiversity, Johann Heinrich Von Thünen Institute, Brunswick, Germany
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas Ceaza, La Serena, Chile
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - Claudia Knief
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany.
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Jiao R, Wu B, Liang Z, Gao P, Gao X. GLV reveal species differences and responses to environment in alpine shrub Rosa sericea complex. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:166146. [PMID: 37595914 DOI: 10.1016/j.scitotenv.2023.166146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/20/2023] [Accepted: 08/06/2023] [Indexed: 08/20/2023]
Abstract
Plant Volatile components are an ecological adaptation mechanism of plants that can reflect species differences and environment information where it is located. The alpine shrub Rosa sericea complex consists of several allied species, which are morphologically similar and difficult to distinguish, they are typical distribution along the elevation in the Himalayas and the Transverse Ranges. We selected two typical areas to find that the different species could be distinguished by their "green leaf volatile components" (GLV) composition as well as their geographical location, and it was evident that species with glands had higher sesquiterpene content. Correlation analysis revealed the relation between volatile components and ecology factors (climate factors, soil factors, phyllospheric microorganisms). Our study adds a new perspective and basis for the environmental adaptations of different species in the alpine shrub Rosa sericea complex from a chemical ecology perspective.
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Affiliation(s)
- Ruifang Jiao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Guangzhou 510650, China
| | - Bohan Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Zhenlong Liang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Gao
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Xinfen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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Byers AK, Condron LM, O'Callaghan M, Waller L, Dickie IA, Wakelin SA. Plant species identity and plant-induced changes in soil physicochemistry-but not plant phylogeny or functional traits - shape the assembly of the root-associated soil microbiome. FEMS Microbiol Ecol 2023; 99:fiad126. [PMID: 37816673 PMCID: PMC10589101 DOI: 10.1093/femsec/fiad126] [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: 05/21/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/12/2023] Open
Abstract
The root-associated soil microbiome contributes immensely to support plant health and performance against abiotic and biotic stressors. Understanding the processes that shape microbial assembly in root-associated soils is of interest in microbial ecology and plant health research. In this study, 37 plant species were grown in the same soil mixture for 10 months, whereupon the root-associated soil microbiome was assessed using amplicon sequencing. From this, the contribution of direct and indirect plant effects on microbial assembly was assessed. Plant species and plant-induced changes in soil physicochemistry were the most significant factors that accounted for bacterial and fungal community variation. Considering that all plants were grown in the same starting soil mixture, our results suggest that plants, in part, shape the assembly of their root-associated soil microbiome via their effects on soil physicochemistry. With the increase in phylogenetic ranking from plant species to class, we observed declines in the degree of community variation attributed to phylogenetic origin. That is, plant-microbe associations were unique to each plant species, but the phylogenetic associations between plant species were not important. We observed a large degree of residual variation (> 65%) not accounted for by any plant-related factors, which may be attributed to random community assembly.
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Affiliation(s)
- Alexa-Kate Byers
- Bioprotection Aotearoa, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | - Leo M Condron
- Bioprotection Aotearoa, Lincoln University, PO Box 85084, Lincoln 7647, New Zealand
| | | | - Lauren Waller
- Biosecurity New Zealand, Ministry for Primary Industries, 34-38 Bowen Street, PO Box 2526, Wellington 6140, New Zealand
| | - Ian A Dickie
- Bioprotection Aotearoa, School of Biological Sciences, University of Canterbury, PO Box 4800, Christchurch 8140, New Zealand
| | - Steve A Wakelin
- Ecology and Environment, Scion Research Ltd, 10 Kyle Street, Riccarton, Christchurch 8011, Canterbury, New Zealand
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Hofmann B, Dreyling L, Dal Grande F, Otte J, Schmitt I. Habitat and tree species identity shape aboveground and belowground fungal communities in central European forests. Front Microbiol 2023; 14:1067906. [PMID: 36950169 PMCID: PMC10025312 DOI: 10.3389/fmicb.2023.1067906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction Trees interact with fungi in mutualistic, saprotrophic, and pathogenic relationships. With their extensive aboveground and belowground structures, trees provide diverse habitats for fungi. Thus, tree species identity is an important driver of fungal community composition in forests. Methods Here we investigate how forest habitat (bark surface vs. soil) and tree species identity (deciduous vs. coniferous) affect fungal communities in two Central European forests. We assess differences and interactions between fungal communities associated with bark surfaces and soil, in forest plots dominated either by Fagus sylvatica, Picea abies, or Pinus sylvestris in two study regions in southwestern and northeastern Germany. Results ITS metabarcoding yielded 3,357 fungal amplicon sequence variants (ASVs) in the northern and 6,088 in the southern region. Overall, soil communities were 4.7 times more diverse than bark communities. Habitat type explained 48-69% of the variation in alpha diversity, while tree species identity explained >1-3%. NMDS ordinations showed that habitat type and host tree species structured the fungal communities. Overall, few fungal taxa were shared between habitats, or between tree species, but the shared taxa were highly abundant. Network analyses, based on co-occurrence patterns, indicate that aboveground and belowground communities form distinct subnetworks. Discussion Our study suggests that habitat (bark versus soil) and tree species identity are important factors structuring fungal communities in temperate European forests. The aboveground (bark-associated) fungal community is currently poorly known, including a high proportion of reads assigned to "unknown Ascomycota" or "unknown Dothideomycetes." The role of bark as a habitat and reservoir of unique fungal diversity in forests has been underestimated.
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Affiliation(s)
- Benjamin Hofmann
- Institute of Ecology, Diversity and Evolution, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Lukas Dreyling
- Institute of Ecology, Diversity and Evolution, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
- Department of Biology, University of Padova, Padua, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Imke Schmitt
- Institute of Ecology, Diversity and Evolution, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
- *Correspondence: Imke Schmitt,
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Li M, Hong L, Ye W, Wang Z, Shen H. Phyllosphere bacterial and fungal communities vary with host species identity, plant traits and seasonality in a subtropical forest. ENVIRONMENTAL MICROBIOME 2022; 17:29. [PMID: 35681245 PMCID: PMC9185928 DOI: 10.1186/s40793-022-00423-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/31/2022] [Indexed: 05/21/2023]
Abstract
BACKGROUND Phyllosphere microbes play important roles in host plant performance and fitness. Recent studies have suggested that tropical and temperate forests harbor diverse phyllosphere bacterial and fungal communities and their assembly is driven by host species identity and plant traits. However, no study has yet examined how seasonality (e.g. dry vs. wet seasons) influences phyllosphere microbial community assembly in natural forests. In addition, in subtropical forests characterized as the transitional zonal vegetation type from tropical to temperate forests, how tree phyllosphere microbial communities are assembled remains unknown. In this study, we quantified bacterial and fungal community structure and diversity on the leaves of 45 tree species with varying phylogenetic identities and importance values within a 20-ha lower subtropical evergreen broad-leaved forest plot in dry and wet seasons. We explored if and how the microbial community assembly varies with host species identity, plant traits and seasonality. RESULTS Phyllosphere microbial communities in the subtropical forest are more abundant and diverse than those in tropical and temperate forests, and the tree species share a "core microbiome" in either bacteria or fungi. Variations in phyllosphere bacterial and fungal community assembly are explained more by host species identity than by seasonality. There is a strong clustering of the phyllosphere microbial assemblage amongst trees by seasonality, and the seasonality effects are more pronounced on bacterial than fungal community assembly. Host traits have different effects on community compositions and diversities of both bacteria and fungi, and among them calcium concentration and importance value are the most powerful explaining variables for bacteria and fungi, respectively. There are significant evolutionary associations between host species and phyllosphere microbiome. CONCLUSIONS Our results suggest that subtropical tree phyllosphere microbial communities vary with host species identity, plant traits and seasonality. Host species identity, compared to seasonality, has greater effects on phyllosphere microbial community assembly, and such effects differ between bacterial and fungal communities. These findings advance our understanding of the patterns and drivers of phyllosphere microbial community assembly in zonal forests at a global scale.
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Affiliation(s)
- Mengjiao Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden/Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lan Hong
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 China
| | - Wanhui Ye
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden/Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhangming Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden/Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Hao Shen
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden/Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
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Leitão F, Pinto G, Amaral J, Monteiro P, Henriques I. New insights into the role of constitutive bacterial rhizobiome and phenolic compounds in two Pinus spp. with contrasting susceptibility to pine pitch canker. TREE PHYSIOLOGY 2022; 42:600-615. [PMID: 34508603 DOI: 10.1093/treephys/tpab119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/06/2021] [Accepted: 09/01/2021] [Indexed: 05/24/2023]
Abstract
The rhizobiome is being increasingly acknowledged as a key player in plant health and breeding strategies. The pine pitch canker (PPC), caused by the fungus Fusarium circinatum, affects pine species with varying susceptibility degrees. Our aims were to explore the bacterial rhizobiome of a susceptible (Pinus radiata) and a resistant (Pinus pinea) species together with other physiological traits, and to analyze shifts upon F. circinatum inoculation. Pinus seedlings were stem inoculated with F. circinatum spores and needle gas exchange and antioxidant-related parameters were analyzed in non-inoculated and inoculated plants. Rhizobiome structure was evaluated through 16S rRNA gene massive parallel sequencing. Species (non-inoculated plants) harbored distinct rhizobiomes (<40% similarity), where P. pinea displayed a rhizobiome with increased abundance of taxa described in suppressive soils, displaying plant growth promoting (PGP) traits and/or anti-fungal activity. Plants of this species also displayed higher levels of phenolic compounds. F. circinatum induced slight changes in the rhizobiome of both species and a negative impact in photosynthetic-related parameters in P. radiata. We concluded that the rhizobiome of each pine species is distinct and higher abundance of bacterial taxa associated to disease protection was registered for the PPC-resistant species. Furthermore, differences in the rhizobiome are paralleled by a distinct content in phenolic compounds, which are also linked to plants' resistance against PPC. This study unveils a species-specific rhizobiome and provides insights to exploit the rhizobiome for plant selection in nurseries and for rhizobiome-based plant-growth-promoting strategies, boosting environmentally friendly disease control strategies.
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Affiliation(s)
- Frederico Leitão
- Biology Department, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Glória Pinto
- Biology Department, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Joana Amaral
- Biology Department, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Pedro Monteiro
- Biology Department, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Isabel Henriques
- Faculty of Science and Technology, Department of Life Sciences and CESAM, University of Coimbra, Coimbra, Portugal
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10
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Cowan JA, Gehring CA, Ilstedt U, Grady KC. Host identity and neighborhood trees affect belowground microbial communities in a tropical rainforest. Trop Ecol 2021. [DOI: 10.1007/s42965-021-00203-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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de Medeiros Azevedo T, Aburjaile FF, Ferreira-Neto JRC, Pandolfi V, Benko-Iseppon AM. The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications. World J Microbiol Biotechnol 2021; 37:206. [PMID: 34708327 DOI: 10.1007/s11274-021-03168-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/05/2021] [Indexed: 11/25/2022]
Abstract
Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.
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Affiliation(s)
- Thamara de Medeiros Azevedo
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Flávia Figueira Aburjaile
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - José Ribamar Costa Ferreira-Neto
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Valesca Pandolfi
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil.
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12
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Bashir I, War AF, Rafiq I, Reshi ZA, Rashid I, Shouche YS. Phyllosphere microbiome: Diversity and functions. Microbiol Res 2021; 254:126888. [PMID: 34700185 DOI: 10.1016/j.micres.2021.126888] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.
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Affiliation(s)
- Iqra Bashir
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India.
| | - Aadil Farooq War
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Iflah Rafiq
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Irfan Rashid
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
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13
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Kaup M, Trull S, Hom EFY. On the move: sloths and their epibionts as model mobile ecosystems. Biol Rev Camb Philos Soc 2021; 96:2638-2660. [PMID: 34309191 PMCID: PMC9290738 DOI: 10.1111/brv.12773] [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: 11/05/2018] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/20/2022]
Abstract
Sloths are unusual mobile ecosystems, containing a high diversity of epibionts living and growing in their fur as they climb slowly through the canopies of tropical forests. These epibionts include poorly studied algae, arthropods, fungi, and bacteria, making sloths likely reservoirs of unexplored biodiversity. This review aims to identify gaps and eliminate misconceptions in our knowledge of sloths and their epibionts, and to identify key questions to stimulate future research into the functions and roles of sloths within a broader ecological and evolutionary context. This review also seeks to position the sloth fur ecosystem as a model for addressing fundamental questions in metacommunity and movement ecology. The conceptual and evidence-based foundation of this review aims to serve as a guide for future hypothesis-driven research into sloths, their microbiota, sloth health and conservation, and the coevolution of symbioses in general.
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Affiliation(s)
- Maya Kaup
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS, 38677-1848, U.S.A
| | - Sam Trull
- The Sloth Institute, Tulemar Gardens, Provincia de Puntarenas, Manuel Antonio, 60601, Costa Rica
| | - Erik F Y Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS, 38677-1848, U.S.A
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14
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Aguirre-von-Wobeser E, Alonso-Sánchez A, Méndez-Bravo A, Villanueva Espino LA, Reverchon F. Barks from avocado trees of different geographic locations have consistent microbial communities. Arch Microbiol 2021; 203:4593-4607. [PMID: 34160629 DOI: 10.1007/s00203-021-02449-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/22/2021] [Accepted: 06/16/2021] [Indexed: 01/07/2023]
Abstract
Bark is a permanent surface for microbial colonization at the interface of trees and the surrounding air, but little is known about its microbial communities. We used shotgun metagenomic sequencing to analyze the bark microbiomes of avocado trees from two orchards, and compared one of them to rhizospheric soil. It was shown that the microbial communities of avocado bark have a well-defined taxonomic structure, with consistent patterns of abundance of bacteria, fungi, and archaea, even in trees from two different locations. Bark microbial communities were distinct from rhizospheric soil, although they showed overlap in some taxa. Thus, avocado bark is a well-defined environment, providing niches for specific taxonomic groups, many of which are also found in other aerial plant tissues. The present in-depth characterization of bark microbial communities can form a basis for their future manipulation for agronomical purposes.
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Affiliation(s)
- Eneas Aguirre-von-Wobeser
- Unidad Regional Hidalgo, CONACYT, Centro de Investigación y Desarrollo, A.C., Blvd. Sta. Catarina s/n, Col. Santiago Tlapacoya, 42110, San Agustin Tlaxiaca, Hidalgo, Mexico.
| | - Alexandro Alonso-Sánchez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Col. El Haya, 91070, Xalapa, Veracruz, Mexico
| | - Alfonso Méndez-Bravo
- Laboratorio Nacional de Análisis y Síntesis Ecológica, CONACYT, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Col. Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacan, Mexico
| | - Luis Alberto Villanueva Espino
- Laboratorio Nacional de Análisis y Síntesis Ecológica, CONACYT, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Col. Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacan, Mexico
| | - Frédérique Reverchon
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Col. El Haya, 91070, Xalapa, Veracruz, Mexico
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15
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Moreira JCF, Brum M, de Almeida LC, Barrera-Berdugo S, de Souza AA, de Camargo PB, Oliveira RS, Alves LF, Rosado BHP, Lambais MR. Asymbiotic nitrogen fixation in the phyllosphere of the Amazon forest: Changing nitrogen cycle paradigms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145066. [PMID: 33582326 DOI: 10.1016/j.scitotenv.2021.145066] [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: 10/19/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Biological nitrogen fixation is a key process for the maintenance of natural ecosystems productivity. In tropical forests, the contribution of asymbiotic nitrogen fixation (ANF) to the nitrogen (N) input has been underestimated, even though few studies have shown that ANF may be as important as symbiotic nitrogen fixation in such environments. The inputs and abiotic modulators of ANF in the Amazon forest are not completely understood. Here, we determined ANF rates and estimated the N inputs from ANF in the phyllosphere, litter and rhizospheric soil of nine tree species in the Amazon forest over time, including an extreme drought period induced by the El Niño-Southern Oscillation. Our data showed that ANF rates in the phyllosphere were 2.8- and 17.6-fold higher than in the litter and rhizospheric soil, respectively, and was highly dependent on tree taxon. Sampling time was the major factor modulating ANF in all forest compartments. At the driest period, ANF rates were approximately 1.8-fold and 13.1-fold higher than at periods with higher rainfall, before and after the extreme drought period, respectively. Tree species was a key modulator of ANF in the phyllosphere, as well as N and Vanadium concentrations. Carbon, molybdenum and vanadium concentrations were significant modulators of ANF in the litter. Based on ANF rates at the three sampling times, we estimated that the N input in the Amazon forest through ANF in the phyllosphere, litter and rhizospheric soil, was between 0.459 and 0.714 kg N ha-1 yr-1. Our results highlight the importance of ANF in the phyllosphere for the N input in the Amazon forest, and suggest that changes in the patterns of ANF driven by large scale climatic events may impact total N inputs and likely alter forest productivity.
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Affiliation(s)
| | - Mauro Brum
- Department of Plant Biology, Programa de Pós Graduação em Ecologia, Institute of Biology, State University of Campinas -UNICAMP, PO Box 6109, 13083-970 Campinas, SP, Brazil
| | - Lidiane Cordeiro de Almeida
- Department of Ecology, IBRAG, Rio de Janeiro State University (UERJ), R. São Francisco Xavier, 524, PHLC, Sala 220, Maracanã, Rio de Janeiro, RJ, Brazil
| | - Silvia Barrera-Berdugo
- Soil Science Department, University of São Paulo, Av. Pádua Dias 11, 13418-900 Piracicaba, SP, Brazil
| | - André Alves de Souza
- Soil Science Department, University of São Paulo, Av. Pádua Dias 11, 13418-900 Piracicaba, SP, Brazil
| | - Plínio Barbosa de Camargo
- Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenário Avenue, Piracicaba, SP 13400-970, Brazil
| | - Rafael Silva Oliveira
- Department of Plant Biology, Programa de Pós Graduação em Ecologia, Institute of Biology, State University of Campinas -UNICAMP, PO Box 6109, 13083-970 Campinas, SP, Brazil
| | - Luciana Ferreira Alves
- Department of Plant Biology, Programa de Pós Graduação em Ecologia, Institute of Biology, State University of Campinas -UNICAMP, PO Box 6109, 13083-970 Campinas, SP, Brazil
| | - Bruno Henrique Pimentel Rosado
- Department of Ecology, IBRAG, Rio de Janeiro State University (UERJ), R. São Francisco Xavier, 524, PHLC, Sala 220, Maracanã, Rio de Janeiro, RJ, Brazil
| | - Marcio Rodrigues Lambais
- Soil Science Department, University of São Paulo, Av. Pádua Dias 11, 13418-900 Piracicaba, SP, Brazil.
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16
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Type II Photosynthetic Reaction Center Genes of Avocado (Persea americana Mill.) Bark Microbial Communities are Dominated by Aerobic Anoxygenic Alphaproteobacteria. Curr Microbiol 2021; 78:2623-2630. [PMID: 33990868 DOI: 10.1007/s00284-021-02525-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 04/28/2021] [Indexed: 10/21/2022]
Abstract
The tree bark environment is an important microbial habitat distributed worldwide on thrillions of trees. However, the microbial communities of tree bark are largely unknown, with most studies on plant aerial surfaces focused on the leaves. Recently, we presented a metagenomic study of bark microbial communities from avocado. In these communities, oxygenic and anoxygenic photosynthesis genes were very abundant, especially when compared to rhizospheric soil from the same trees. In this work, Evolutionary Placement Algorithm analysis was performed on metagenomic reads orthologous to the PufLM gene cluster, encoding for the bacterial type II photosynthetic reaction center. These photosynthetic genes were found affiliated to different groups of bacteria, mostly aerobic anoxygenic photosynthetic Alphaproteobacteria, including Sphingomonas, Methylobacterium and several Rhodospirillales. These results suggest that anoxygenic photosynthesis in avocado bark microbial communities functions primarily as additional energy source for heterotrophic growth. Together with our previous results, showing a large abundance of cyanobacteria in these communities, a picture emerges of the tree holobiont, where light penetrating the tree canopies and reaching the inner stems, including the trunk, is probably utilized by cyanobacteria for oxygenic photosynthesis, and the far-red light aids the growth of aerobic anoxygenic photosynthetic bacteria.
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17
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Genitsaris S, Stefanidou N, Leontidou K, Matsi T, Karamanoli K, Mellidou I. Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems. Microorganisms 2020; 8:E1708. [PMID: 33142812 PMCID: PMC7692439 DOI: 10.3390/microorganisms8111708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/23/2022] Open
Abstract
The aim of the study was to investigate the bacterial community diversity and structure by means of 16S rRNA gene high-throughput amplicon sequencing, in the rhizosphere and phyllosphere of halophytes and drought-tolerant plants in Mediterranean ecosystems with different soil properties. The locations of the sampled plants included alkaline, saline-sodic soils, acidic soils, and the volcanic soils of Santorini Island, differing in soil fertility. Our results showed high bacterial richness overall with Proteobacteria and Actinobacteria dominating in terms of OTUs number and indicated that variable bacterial communities differed depending on the plant's compartment (rhizosphere and phyllosphere), the soil properties and location of sampling. Furthermore, a shared pool of generalist bacterial taxa was detected independently of sampling location, plant species, or plant compartment. We conclude that the rhizosphere and phyllosphere of native plants in stressed Mediterranean ecosystems consist of common bacterial assemblages contributing to the survival of the plant, while at the same time the discrete soil properties and environmental pressures of each habitat drive the development of a complementary bacterial community with a distinct structure for each plant and location. We suggest that this trade-off between generalist and specialist bacterial community is tailored to benefit the symbiosis with the plant.
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Affiliation(s)
- Savvas Genitsaris
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Kleopatra Leontidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Theodora Matsi
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Ifigeneia Mellidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
- Institute of Plant Breeding and Genetic Resources, HAO ELGO-DEMETER, 57 001 Thermi, Greece
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18
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Mina D, Pereira JA, Lino-Neto T, Baptista P. Epiphytic and Endophytic Bacteria on Olive Tree Phyllosphere: Exploring Tissue and Cultivar Effect. MICROBIAL ECOLOGY 2020; 80:145-157. [PMID: 31965223 DOI: 10.1007/s00248-020-01488-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/09/2020] [Indexed: 06/10/2023]
Abstract
Variation on bacterial communities living in the phyllosphere as epiphytes and endophytes has been attributed to plant host effects. However, there is contradictory or inconclusive evidence regarding the effect of plant genetics (below the species' level) and of plant tissue type on phyllosphere bacterial community assembly, in particular when epiphytes and endophytes are considered simultaneously. Here, both surface and internal bacterial communities of two olive (Olea europaea) cultivars were evaluated in twigs and leaves by molecular identification of cultivable isolates, with an attempt to answer these questions. Overall, Proteobacteria, Actinobacteria and Firmicutes were the dominant phyla, being epiphytes more diverse and abundant than endophytes. Host genotype (at cultivar level) had a structuring effect on the composition of bacterial communities and, in a similar way, for both epiphytes and endophytes. Plant organ (leaf vs. twig) control of the bacterial communities was less evident when compared with plant genotype and with a greater influence on epiphytic than on endophytic community structure. Each olive genotype/plant organ was apparently selective towards specific bacterial operational taxonomic units (OTUs), which may lead to specific feedbacks on fitness of plant genotypes. Bacterial recruitment was observed to happen mainly within epiphytes than in endophytes and in leaves as compared with twigs. Such host specificity suggested that the benefits derived from the plant-bacteria interaction should be considered at genetic levels below the species.
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Affiliation(s)
- Diogo Mina
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Braganca, Portugal
| | - José Alberto Pereira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Braganca, Portugal
| | - Teresa Lino-Neto
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Paula Baptista
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Braganca, Portugal.
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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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20
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Lajoie G, Maglione R, Kembel SW. Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest. MICROBIOME 2020; 8:70. [PMID: 32438916 PMCID: PMC7243311 DOI: 10.1186/s40168-020-00844-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/17/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND The phyllosphere is an important microbial habitat, but our understanding of how plant hosts drive the composition of their associated leaf microbial communities and whether taxonomic associations between plants and phyllosphere microbes represent adaptive matching remains limited. In this study, we quantify bacterial functional diversity in the phyllosphere of 17 tree species in a diverse neotropical forest using metagenomic shotgun sequencing. We ask how hosts drive the functional composition of phyllosphere communities and their turnover across tree species, using host functional traits and phylogeny. RESULTS Neotropical tree phyllosphere communities are dominated by functions related to the metabolism of carbohydrates, amino acids, and energy acquisition, along with environmental signalling pathways involved in membrane transport. While most functional variation was observed within communities, there is non-random assembly of microbial functions across host species possessing different leaf traits. Metabolic functions related to biosynthesis and degradation of secondary compounds, along with signal transduction and cell-cell adhesion, were particularly important in driving the match between microbial functions and host traits. These microbial functions were also evolutionarily conserved across the host phylogeny. CONCLUSIONS Functional profiling based on metagenomic shotgun sequencing offers evidence for the presence of a core functional microbiota across phyllosphere communities of neotropical trees. While functional turnover across phyllosphere communities is relatively small, the association between microbial functions and leaf trait gradients among host species supports a significant role for plant hosts as selective filters on phyllosphere community assembly. This interpretation is supported by the presence of phylogenetic signal for the microbial traits driving inter-community variation across the host phylogeny. Taken together, our results suggest that there is adaptive matching between phyllosphere microbes and their plant hosts. Video abstract.
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Affiliation(s)
- Geneviève Lajoie
- Département des sciences biologiques, Université du Québec à Montréal, 141, Avenue du Président-Kennedy, Montréal, Quebec, H2X 1Y4 Canada
| | - Rémi Maglione
- Département des sciences biologiques, Université du Québec à Montréal, 141, Avenue du Président-Kennedy, Montréal, Quebec, H2X 1Y4 Canada
| | - Steven W. Kembel
- Département des sciences biologiques, Université du Québec à Montréal, 141, Avenue du Président-Kennedy, Montréal, Quebec, H2X 1Y4 Canada
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21
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Tzec-Interián JA, Desgarennes D, Carrión G, Monribot-Villanueva JL, Guerrero-Analco JA, Ferrera-Rodríguez O, Santos-Rodríguez DL, Liahut-Guin N, Caballero-Reyes GE, Ortiz-Castro R. Characterization of plant growth-promoting bacteria associated with avocado trees (Persea americana Miller) and their potential use in the biocontrol of Scirtothrips perseae (avocado thrips). PLoS One 2020; 15:e0231215. [PMID: 32267901 PMCID: PMC7141680 DOI: 10.1371/journal.pone.0231215] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/18/2020] [Indexed: 11/25/2022] Open
Abstract
Plants interact with a great variety of microorganisms that inhabit the rhizosphere or the epiphytic and endophytic phyllosphere and that play critical roles in plant growth as well as the biocontrol of phytopathogens and insect pests. Avocado fruit damage caused by the thrips species Scirtothrips perseae leads to economic losses of 12–51% in many countries. In this study, a screening of bacteria associated with the rhizosphere or endophytic phyllosphere of avocado roots was performed to identify bacterial isolates with plant growth-promoting activity in vitro assays with Arabidopsis seedlings and to assess the biocontrol activity of the isolates against Scirtothrips perseae. The isolates with beneficial, pathogenic and/or neutral effects on Arabidopsis seedlings were identified. The plant growth-promoting bacteria were clustered in two different groups (G1 and G3B) based on their effects on root architecture and auxin responses, particularly bacteria of the Pseudomonas genus (MRf4-2, MRf4-4 and TRf2-7) and one Serratia sp. (TS3-6). Twenty strains were selected based on their plant growth promotion characteristics to evaluate their potential as thrips biocontrol agents. Analyzing the biocontrol activity of S. perseae, it was identified that Chryseobacterium sp. shows an entomopathogenic effect on avocado thrips survival. Through the metabolic profiling of compounds produced by bacteria with plant growth promotion activity, bioactive cyclodipeptides (CDPs) that could be responsible for the plant growth-promoting activity in Arabidopsis were identified in Pseudomonas, Serratia and Stenotrophomonas. This study unravels the diversity of bacteria from the avocado rhizosphere and highlights the potential of a unique isolate to achieve the biocontrol of S. perseae.
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Affiliation(s)
| | - Damaris Desgarennes
- Red de Biodiversidad y Sistemática, Instituto de Ecología, Xalapa, Veracruz, México
| | - Gloria Carrión
- Red de Biodiversidad y Sistemática, Instituto de Ecología, Xalapa, Veracruz, México
- * E-mail: (ROC); (GC)
| | | | | | | | | | - Nut Liahut-Guin
- Red de Biodiversidad y Sistemática, Instituto de Ecología, Xalapa, Veracruz, México
| | | | - Randy Ortiz-Castro
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, Xalapa, Veracruz, México
- Catedratico-CONACyT en el Instituto de Ecología A. C., Xalapa, Veracruz, México
- * E-mail: (ROC); (GC)
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22
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Massoni J, Bortfeld-Miller M, Jardillier L, Salazar G, Sunagawa S, Vorholt JA. Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species. THE ISME JOURNAL 2020; 14:245-258. [PMID: 31624344 PMCID: PMC6908658 DOI: 10.1038/s41396-019-0531-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 09/18/2019] [Accepted: 09/24/2019] [Indexed: 01/29/2023]
Abstract
Bacteria colonizing the aerial parts of plants (phyllosphere) are linked to the biology of their host. They impact plant-pathogen interactions and may influence plant reproduction. Past studies have shown differences in composition and structure of the leaf, flower, and host microbiota, but an investigation of the impact of individual taxa on these variations remains to be tested. Such information will help to evaluate disparities and to better understand the biology and evolution of the plant-microbe associations. In the present study, we investigated the community structure, occupancy of host and organ, and the prevalence of phyllosphere bacteria from three host species collected at the same location. Almost all (98%) of bacterial taxa detected in the phyllosphere were not only shared across leaves and flowers, or different plant species but also had a conserved prevalence across sub-environments of the phyllosphere. We also found nonrandom associations of the phylogenetic diversity of phyllosphere bacteria. These results suggest that the phyllosphere microbiota is more conserved than previously acknowledged, and dominated by generalist bacteria adapted to environmental heterogeneity through evolutionary conserved traits.
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Affiliation(s)
- Julien Massoni
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland.
- Center for Adaptation to a Changing Environment, ETH Zurich, 8092, Zurich, Switzerland.
| | - Miriam Bortfeld-Miller
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Ludwig Jardillier
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Julia A Vorholt
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland.
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23
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Su P, Zhang D, Zhang Z, Chen A, Hamid MR, Li C, Du J, Cheng J, Tan X, Zhen L, Zhai Z, Tang W, Chen J, Zhou X, Liu Y. Characterization of Rhodopseudomonas palustris population dynamics on tobacco phyllosphere and induction of plant resistance to Tobacco mosaic virus. Microb Biotechnol 2019; 12:1453-1463. [PMID: 31566880 PMCID: PMC6801143 DOI: 10.1111/1751-7915.13486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/16/2019] [Accepted: 08/26/2019] [Indexed: 11/29/2022] Open
Abstract
Although many biocontrol bacteria can be used to improve plant tolerance to stresses and to promote plant growth, the hostile environmental conditions on plant phyllosphere and the limited knowledge on bacterial colonization on plant phyllosphere minimized the beneficial effects produced by the biocontrol bacteria. Rhodopseudomonas palustris strain GJ-22 is known as a phyllosphere biocontrol agent. In this paper, we described detailed processes of strain GJ-22 colony establishment at various colonization stages. Four different types of bacterial colonies, Type 1, scattered single cells; Type 2, small cell clusters; Type 3, small cell aggregates; and Type 4, large cell aggregates, were observed in the course of bacterial colonization. We categorized bacterial colonization into four phases, which were, Phase I: bacterial colony exists as Type 1 and cell population reduced quickly; Phase II: Type 1 evolved into Type 2 and cell population remained steady; Phase III: Type 3 arose and replaced Type 2, and cell population expanded slowly; and Phase IV: Type 3 matured into Type 4 and cell population increased quickly. We have shown that the preferable location sites of bacterial aggregates on leaf phyllosphere are grooves between plant epidermal cells. Analyses of expressions of plant defence-related genes showed that, starting from Phase III, bacterial cells in the Type 3 and Type 4 colonies produced unidentified signals to induce host defence against Tobacco mosaic virus infection. In addition, we determined the crucial role of aggregates formation of GJ-22 cell on plant phyllosphere in terms of bacterial cell stress tolerance and ISR (induced systemic resistance) priming. To our knowledge, this is the first report focused on the colonization process of a phyllosphere biocontrol agent and gave a clear description on the morphological shift of bacterial colony on phyllosphere.
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Affiliation(s)
- Pin Su
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
| | - Deyong Zhang
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
| | - Zhuo Zhang
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
| | - Ang Chen
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
| | - Muhammad Rizwan Hamid
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
| | - Chenggang Li
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
| | - Jiao Du
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
| | - Ju'e Cheng
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
| | - Xinqiu Tan
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
| | - Limin Zhen
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
| | - Zhongying Zhai
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
| | - Wen Tang
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
| | - Jin Chen
- College of Bioscience and BiotechnologyHunan Agricultural UniversityChangsha410128China
| | - Xuguo Zhou
- Department of EntomologyUniversity of KentuckyLexingtonKY40546USA
| | - Yong Liu
- Hunan Plant Protection InstituteHunan Academy of Agricultural SciencesChangsha410125China
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24
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Camacho-Montealegre CM, Rodrigues EM, Tótola MR. Microbial diversity and bioremediation of rhizospheric soils from Trindade Island - Brazil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 236:358-364. [PMID: 30739041 DOI: 10.1016/j.jenvman.2019.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/17/2019] [Accepted: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Pristine environments may harbor complex microbial communities with metabolic potential for use in bioremediation of organic pollutants. This study aimed to evaluate crude oil biodegradation by microbial communities present in rhizospheric soils of Bulbostylis nesiotis and Cyperus atlanticus on Trindade Island and the compositional structure of these communities. After 60 days under aerobic conditions, Total Petroleum Hydrocarbon biodegradation ranged from 66 to 75%, depending on the plant species and the origin of the soil samples. There was no response of petroleum biodegradation to fertilization with N:P:K (80:160:80 mg dm-3). Soil contamination with crude oil did not necessarily reduce microbial diversity. The richness and diversity increased in contaminated soils in some specific situations. We conclude that microbial communities from pristine soils have the ability to remove hydrocarbons through biodegradation and that Bulbostylis nesiotis and Cyperus atlanticus inhabiting Trindade Island harbor rhizospheric microbial communities with potential for application in rhizoremediation.
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Affiliation(s)
- Celia Marcela Camacho-Montealegre
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Edmo Montes Rodrigues
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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25
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Amend AS, Cobian GM, Laruson AJ, Remple K, Tucker SJ, Poff KE, Antaky C, Boraks A, Jones CA, Kuehu D, Lensing BR, Pejhanmehr M, Richardson DT, Riley PP. Phytobiomes are compositionally nested from the ground up. PeerJ 2019; 7:e6609. [PMID: 30918757 PMCID: PMC6428039 DOI: 10.7717/peerj.6609] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/04/2019] [Indexed: 11/29/2022] Open
Abstract
Plant-associated microbes are critical players in host health, fitness and productivity. Despite microbes’ importance in plants, seeds are mostly sterile, and most plant microbes are recruited from an environmental pool. Surprisingly little is known about the processes that govern how environmental microbes assemble on plants in nature. In this study we examine how bacteria are distributed across plant parts, and how these distributions interact with spatial gradients. We sequenced amplicons of bacteria from the surfaces of six plant parts and adjacent soil of Scaevola taccada, a common beach shrub, along a 60 km transect spanning O’ahu island’s windward coast, as well as within a single intensively-sampled site. Bacteria are more strongly partitioned by plant part as compared with location. Within S. taccada plants, microbial communities are highly nested: soil and rhizosphere communities contain much of the diversity found elsewhere, whereas reproductive parts fall at the bottom of the nestedness hierarchy. Nestedness patterns suggest either that microbes follow a source/sink gradient from the ground up, or else that assembly processes correlate with other traits, such as tissue persistence, that are vertically stratified. Our work shines light on the origins and determinants of plant-associated microbes across plant and landscape scales.
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Affiliation(s)
- Anthony S Amend
- Department of Botany, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Gerald M Cobian
- Department of Botany, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Aki J Laruson
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Kristina Remple
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Sarah J Tucker
- Marine Biology Program, University of Hawaii at Manoa, Honolulu, HI, United States of America.,Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Kirsten E Poff
- Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Carmen Antaky
- Department of Natural Resources and Environmental Management, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Andre Boraks
- Department of Botany, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Casey A Jones
- Department of Botany, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Donna Kuehu
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Becca R Lensing
- Marine Biology Program, University of Hawaii at Manoa, Honolulu, HI, United States of America.,Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Mersedeh Pejhanmehr
- Department of Botany, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Daniel T Richardson
- Department of Natural Resources and Environmental Management, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Paul P Riley
- Department of Natural Resources and Environmental Management, University of Hawaii at Manoa, Honolulu, HI, United States of America
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26
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Mhuireach GÁ, Betancourt-Román CM, Green JL, Johnson BR. Spatiotemporal Controls on the Urban Aerobiome. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00043] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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27
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Chi Y, Lin Y, Lu Y, Huang Q, Ye G, Dong S. Gut microbiota dysbiosis correlates with a low-dose PCB126-induced dyslipidemia and non-alcoholic fatty liver disease. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:274-282. [PMID: 30412872 DOI: 10.1016/j.scitotenv.2018.10.387] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/24/2018] [Accepted: 10/28/2018] [Indexed: 06/08/2023]
Abstract
There is growing evidence that polychlorinated biphenyl 126 (PCB126) not only has adverse effects on host health but also has the ability to shift gut microbiota, which is recently recognized as a crucial factor determining numerous physiological processes. However, the interplay between the gut microbiota and host health remains largely unknown. Herein, adult female C57BL/6 mice were orally exposed to environmentally relevant low-dose of PCB126, at 50 μg/kg body weight once per week for 6 weeks. This study aims to illuminate how PCB126 influences gut microbiota variations and host disorders and to further identify the correlation between the gut microbiota and metabolic markers of host disorders. Obtained results demonstrated that the PCB126 administration induced gut microbiota dysbiosis in mice, with changes both in the gut microbiota constitution and structure. PCB126 administration also simultaneously altered the physiological status of serum and liver, as evaluated by dyslipidemia, liver lipid accumulation and injury, and non-alcoholic fatty liver disease. Importantly, Spearman's correlation analysis suggested that several specific bacterial taxa were positively and significantly related to metabolic markers of the mentioned disorders. Moreover, based on the co-occurrence network map, some of the bacterial taxa may synergistically regulate host physiology. This work provides new insight into the mechanism underlying the interaction between the gut microbiota and host disorders. It is expected that gut microbiota modulation should be another novel way used for the prevention and treatment of PCB126-triggered diseases.
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Affiliation(s)
- Yulang Chi
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yanyang Lu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qiansheng Huang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guozhu Ye
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Sijun Dong
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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28
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Rogers TJ, Leppanen C, Brown V, Fordyce JA, LeBude A, Ranney T, Simberloff D, Cregger MA. Exploring variation in phyllosphere microbial communities across four hemlock species. Ecosphere 2018. [DOI: 10.1002/ecs2.2524] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Timothy J. Rogers
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee 37831 USA
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - Christy Leppanen
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - Veronica Brown
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - James A. Fordyce
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - Anthony LeBude
- Department of Horticultural Science North Carolina State University Mills River North Carolina 28759 USA
| | - Thomas Ranney
- Department of Horticultural Science North Carolina State University Mills River North Carolina 28759 USA
| | - Daniel Simberloff
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
| | - Melissa A. Cregger
- Biosciences Division Oak Ridge National Laboratory Oak Ridge Tennessee 37831 USA
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996 USA
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29
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Padgurschi MCG, Vieira SA, Stefani EJF, Nardoto GB, Joly CA. Nitrogen input by bamboos in neotropical forest: a new perspective. PeerJ 2018; 6:e6024. [PMID: 30519513 PMCID: PMC6275114 DOI: 10.7717/peerj.6024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 10/24/2018] [Indexed: 11/20/2022] Open
Abstract
Background Nitrogen (N) is an important macronutrient that controls the productivity of ecosystems and biological nitrogen fixation (BNF) is a major source of N in terrestrial systems, particularly tropical forests. Bamboo dominates theses forests, but our knowledge regarding the role of bamboo in ecosystem functioning remains in its infancy. We investigated the importance of a native bamboo species to the N cycle of a Neotropical forest. Methods We selected 100 sample units (100 m2 each) in a pristine montane Atlantic Forest, in Brazil. We counted all the clumps and live culms of Merostachys neesii bamboo and calculated the specific and total leaf area, as well as litter production and respective N content. Potential N input was estimated based on available data on BNF rates for the same bamboo species, whose N input was then contextualized using information on N cycling components in the study area. Results With 4,000 live culms ha-1, the native bamboo may contribute up to 11.7 kg N ha-1 during summer (January to March) and 19.6 kg N ha-1 in winter (July to September). When extrapolated for annual values, M. neesii could contribute more than 60 kg N ha-1y-1. Discussion The bamboo species' contribution to N input may be due to its abundance (habitat availability for microbial colonization) and the composition of the free-living N fixer community on its leaves (demonstrated in previous studies). Although some N is lost during decomposition, this input could mitigate the N deficit in the Atlantic Forest studied by at least 27%. Our findings suggest that M. neesii closely regulates N input and may better explain the high diversity and carbon stocks in the area. This is the first time that a study has investigated BNF using free-living N fixers on the phyllosphere of bamboo.
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Affiliation(s)
- Maíra C G Padgurschi
- Plant Biology Department, State University of Campinas, Campinas, São Paulo, Brazil
| | - Simone A Vieira
- Center for Environmental Studies and Research, State University of Campinas, Campinas, São Paulo, Brazil
| | - Edson J F Stefani
- Plant Biology Department, State University of Campinas, Campinas, São Paulo, Brazil
| | | | - Carlos A Joly
- Plant Biology Department, State University of Campinas, Campinas, São Paulo, Brazil
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30
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Lei S, Xu X, Cheng Z, Xiong J, Ma R, Zhang L, Yang X, Zhu Y, Zhang B, Tian B. Analysis of the community composition and bacterial diversity of the rhizosphere microbiome across different plant taxa. Microbiologyopen 2018; 8:e00762. [PMID: 30565881 PMCID: PMC6562120 DOI: 10.1002/mbo3.762] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 10/07/2018] [Accepted: 10/08/2018] [Indexed: 12/23/2022] Open
Abstract
Rhizobacteria play an important role in bridging the soil and plant microbiomes and improving the health and growth of plants. In this study, the bacterial community structures and compositions of rhizosphere microbiomes associated with six plant species, representing two orders and three families of wild plants grown in the same field, were evaluated. The six plant species examined harbored a core and similar bacterial communities of the rhizosphere microbiome, which was dominated by members of Rhizobiales, Sphingomonadales, Burkholderiales, and Xanthomonadales of Proteobacteria, Subgroup 4 of Acidobacteria, and Sphingobacteriales of Bacteroidetes. Plant species had a significant effect on the microbial composition and Operational Taxonomic Unit (OTU) abundance of the rhizosphere microbiome. Statistical analysis indicated a significant differential OTU richness (Chao1, p < 0.05) and bacterial diversity (Shannon index, p < 0.0001) of the rhizosphere microbiome at the plant species, genus, or families levels. The paralleled samples from the same plant species in the PCoA and hierarchical cluster analysis demonstrated a clear tendency to group together, although the samples were not strictly separated according to their taxonomic divergence at the family or order level. The CAP analysis revealed a great proportion (44.85%) of the variations on bacterial communities could be attributed to the plant species. The results demonstrated that largely conserved and taxonomically narrow bacterial communities of the rhizosphere microbiome existed around the plant root. The bacterial communities and diversity of the rhizosphere microbiome were significantly related to the plant taxa, at least at the species levels.
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Affiliation(s)
- Shaonan Lei
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Engineering Research Center of Industrial Microbiology of Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Xiaohong Xu
- Library, Fujian Normal University, Fuzhou, China
| | - Zhiqiang Cheng
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Engineering Research Center of Industrial Microbiology of Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Juan Xiong
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Engineering Research Center of Industrial Microbiology of Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Rongqin Ma
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Lanlan Zhang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xiaorong Yang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yunxi Zhu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | | | - Baoyu Tian
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Engineering Research Center of Industrial Microbiology of Ministry of Education, Fujian Normal University, Fuzhou, China
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31
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Wallace J, Laforest-Lapointe I, Kembel SW. Variation in the leaf and root microbiome of sugar maple ( Acer saccharum) at an elevational range limit. PeerJ 2018; 6:e5293. [PMID: 30128178 PMCID: PMC6097496 DOI: 10.7717/peerj.5293] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/02/2018] [Indexed: 11/20/2022] Open
Abstract
Background Bacteria, archaea, viruses and fungi live in various plant compartments including leaves and roots. These plant-associated microbial communities have many effects on host fitness and function. Global climate change is impacting plant species distributions, a phenomenon that will affect plant-microbe interactions both directly and indirectly. In order to predict plant responses to global climate change, it will be crucial to improve our understanding of plant-microbe interactions within and at the edge of plant species natural ranges. While microbes affect their hosts, in turn the plant’s attributes and the surrounding environment drive the structure and assembly of the microbial communities themselves. However, the patterns and dynamics of these interactions and their causes are poorly understood. Methods In this study, we quantified the microbial communities of the leaves and roots of seedlings of the deciduous tree species sugar maple (Acer saccharum Marshall) within its natural range and at the species’ elevational range limit at Mont-Mégantic, Quebec. Using high-throughput DNA sequencing, we quantified the bacterial and fungal community structure in four plant compartments: the epiphytes and endophytes of leaves and roots. We also quantified endophytic fungal communities in roots. Results The bacterial and fungal communities of A. saccharum seedlings differ across elevational range limits for all four plant compartments. Distinct microbial communities colonize each compartment, although the microbial communities inside a plant’s structure (endophytes) were found to be a subset of the communities found outside the plant’s structure (epiphytes). Plant-associated bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes while the main fungal taxa present were Ascomycota. Discussion We demonstrate that microbial communities associated with sugar maple seedlings at the edge of the species’ elevational range differ from those within the natural range. Variation in microbial communities differed among plant components, suggesting the importance of each compartment’s exposure to changes in biotic and abiotic conditions in determining variability in community structure. These findings provide a greater understanding of the ecological processes driving the structure and diversity of plant-associated microbial communities within and at the edge of a plant species range, and suggest the potential for biotic interactions between plants and their associated microbiota to influence the dynamics of plant range edge boundaries and responses to global change.
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Affiliation(s)
- Jessica Wallace
- Département des sciences biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Isabelle Laforest-Lapointe
- Département des sciences biologiques, Université du Québec à Montréal, Montréal, Québec, Canada.,Departments of Physiology and Pharmacology, and Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Steven W Kembel
- Département des sciences biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
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32
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Durand A, Maillard F, Alvarez-Lopez V, Guinchard S, Bertheau C, Valot B, Blaudez D, Chalot M. Bacterial diversity associated with poplar trees grown on a Hg-contaminated site: Community characterization and isolation of Hg-resistant plant growth-promoting bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 622-623:1165-1177. [PMID: 29890585 DOI: 10.1016/j.scitotenv.2017.12.069] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 05/19/2023]
Abstract
Industrial waste dumps are rarely colonized by vegetation after they have been abandoned, indicating biological infertility. Revegetation of industrial tailings dumps is thus necessary to prevent wind erosion, metal leaching and has been shown to restore soil functions and ecosystem services. However, little is known about the microbial colonization and community structure of vegetated tailings following the application of restoration technologies. In this study, we investigated the rhizosphere and phyllosphere bacterial communities of a poplar tree plantation within a phytomanagement-based restoration program of a Hg-contaminated site. We used Illumina-based sequencing combined with culture-dependent approaches to describe plant-associated bacterial communities and to isolate growth-promoting bacteria (PGPB) and Hg-resistant bacteria. The genus Streptomyces was highly specific to the root community, accounting for 24.4% of the relative abundance but only representing 0.8% of the soil community, whereas OTUs from the Chloroflexi phylum were essentially detected in the soil community. Aboveground habitats were dominated by bacteria from the Deinococcus-Thermus phylum, which were not detected in belowground habitats. Leaf and stem habitats were characterized by several dominant OTUs, such as those from the phylum Firmicutes in the stems or from the genera Methylobacterium, Kineococcus, Sphingomonas and Hymenobacter in the leaves. Belowground habitats hosted more cultivable Hg-resistant bacteria than aboveground habitats and more Hg-resistant bacteria were found on the episphere than in endospheric habitats. Hg-resistant isolates exhibiting plant growth-promoting (PGP) traits, when used as inoculants of Capsicum annuum, were shown to increase its root dry biomass but not Hg concentration. The N2-fixing and Hg-resistant species Pseudomonas graminis, observed in the poplar phyllosphere, may be a key microorganism for the restoration of industrial tailings dumps.
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Affiliation(s)
- Alexis Durand
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - François Maillard
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Vanessa Alvarez-Lopez
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Sarah Guinchard
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Coralie Bertheau
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Benoit Valot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France
| | - Damien Blaudez
- Université de Lorraine, UMR CNRS 7360 Laboratoire Interdisciplinaire des Environnements Continentaux, Faculté des Sciences et Technologies, BP 70239, 54506, Vandœuvre-lès-Nancy, France
| | - Michel Chalot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211 Montbéliard, France; Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre-les-Nancy, France.
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Arrigoni E, Antonielli L, Pindo M, Pertot I, Perazzolli M. Tissue age and plant genotype affect the microbiota of apple and pear bark. Microbiol Res 2018; 211:57-68. [PMID: 29705206 DOI: 10.1016/j.micres.2018.04.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/06/2018] [Indexed: 01/16/2023]
Abstract
Plant tissues host complex fungal and bacterial communities, and their composition is determined by host traits such as tissue age, plant genotype and environmental conditions. Despite the importance of bark as a possible reservoir of plant pathogenic microorganisms, little is known about the associated microbial communities. In this work, we evaluated the composition of fungal and bacterial communities in the pear (Abate and Williams cultivars) and apple (Golden Delicious and Gala cultivars) bark of three/four-year-old shoots (old bark) or one-year-old shoots (young bark), using a meta-barcoding approach. The results showed that both fungal and bacterial communities are dominated by genera with ubiquitous attitudes, such as Aureobasidium, Cryptococcus, Deinococcus and Hymenobacter, indicating intense microbial migration to surrounding environments. The shoot age, plant species and plant cultivar influenced the composition of bark fungal and bacterial communities. In particular, bark communities included potential biocontrol agents that could maintain an equilibrium with potential plant pathogens. The abundance of fungal (e.g. Alternaria, Penicillium, Rosellinia, Stemphylium and Taphrina) and bacterial (e.g. Curtobacterium and Pseudomonas) plant pathogens was affected by bark age and host genotype, as well as those of fungal genera (e.g. Arthrinium, Aureobasidium, Rhodotorula, Sporobolomyces) and bacterial genera (e.g. Bacillus, Brevibacillus, Methylobacterium, Sphingomonas and Stenotrophomonas) with possible biocontrol and plant growth promotion properties.
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Affiliation(s)
- Elena Arrigoni
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Italy; Department of Agricultural and Environmental Sciences, University of Udine, Via delle Scienze 206, 33100, Udine, Italy
| | - Livio Antonielli
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology, Konrad-Lorenz-Strasse 24, 3430, Tulln an der Donau, Austria
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Ilaria Pertot
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Italy; Centre for Agriculture, Food and the Environment, University of Trento, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Michele Perazzolli
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Italy.
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A New Method for Characterizing Bark Microrelief Using 3D Vision Systems. FORESTS 2018. [DOI: 10.3390/f9010030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Griffin EA, Carson WP. Tree Endophytes: Cryptic Drivers of Tropical Forest Diversity. ENDOPHYTES OF FOREST TREES 2018. [DOI: 10.1007/978-3-319-89833-9_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity. mSystems 2017; 2:mSystems00087-17. [PMID: 29238751 PMCID: PMC5715107 DOI: 10.1128/msystems.00087-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/14/2017] [Indexed: 02/01/2023] Open
Abstract
In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria. Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.
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Physical Conditions Regulate the Fungal to Bacterial Ratios of a Tropical Suspended Soil. FORESTS 2017. [DOI: 10.3390/f8120474] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Andreote FD, Pereira e Silva MDC. Microbial communities associated with plants: learning from nature to apply it in agriculture. Curr Opin Microbiol 2017; 37:29-34. [DOI: 10.1016/j.mib.2017.03.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/22/2017] [Indexed: 01/20/2023]
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Lambais MR, Barrera SE, Santos EC, Crowley DE, Jumpponen A. Phyllosphere Metaproteomes of Trees from the Brazilian Atlantic Forest Show High Levels of Functional Redundancy. MICROBIAL ECOLOGY 2017; 73:123-134. [PMID: 27853840 DOI: 10.1007/s00248-016-0878-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 10/10/2016] [Indexed: 05/11/2023]
Abstract
The phyllosphere of the Brazilian Atlantic Forest has been estimated to contain several million bacterial species that are associated with approximately 20000 plant species. Despite the high bacterial diversity in the phyllosphere, the function of these microorganisms and the mechanisms driving their community assembly are largely unknown. In this study, we characterized the bacterial communities in the phyllospheres of four tree species of the Atlantic Forest (Mollinedia schottiana, Ocotea dispersa, Ocotea teleiandra, and Tabebuia serratifolia) and their metaproteomes to examine the basic protein functional groups expressed in the phyllosphere. Bacterial community analyses using 16S rRNA gene sequencing confirmed prior observations that plant species harbor distinct bacterial communities and that plants of the same taxon have more similar communities than more distantly related taxa. Using LC-ESI-Q-TOF, we identified 216 nonredundant proteins, based on 3503 peptide mass spectra. Most protein families were shared among the phyllosphere communities, suggesting functional redundancy despite differences in the species compositions of the bacterial communities. Proteins involved in glycolysis and anaerobic carbohydrate metabolism, solute transport, protein metabolism, cell motility, stress and antioxidant responses, nitrogen metabolism, and iron homeostasis were among the most frequently detected. In contrast to prior studies on crop plants and Arabidopsis, a low abundance of OTUs related to Methylobacterium and no proteins associated with the metabolism of one-carbon molecules were detected in the phyllospheres of the tree species studied here. Our data suggest that even though the phyllosphere bacterial communities of different tree species are phylogenetically diverse, their metaproteomes are functionally convergent with respect to traits required for survival on leaf surfaces.
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Affiliation(s)
- M R Lambais
- Departamento de Ciência do Solo, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil.
| | - S E Barrera
- Departamento de Ciência do Solo, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - E C Santos
- Departamento de Ciência do Solo, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - D E Crowley
- Department of Environmental Sciences, University of California, 900 University Ave, Riverside, CA, 92521, USA
| | - A Jumpponen
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS, 66506, USA
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Mhuireach G, Johnson BR, Altrichter AE, Ladau J, Meadow JF, Pollard KS, Green JL. Urban greenness influences airborne bacterial community composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 571:680-7. [PMID: 27418518 DOI: 10.1016/j.scitotenv.2016.07.037] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 05/06/2023]
Abstract
Urban green space provides health benefits for city dwellers, and new evidence suggests that microorganisms associated with soil and vegetation could play a role. While airborne microorganisms are ubiquitous in urban areas, the influence of nearby vegetation on airborne microbial communities remains poorly understood. We examined airborne microbial communities in parks and parking lots in Eugene, Oregon, using high-throughput sequencing of the bacterial 16S rRNA gene on the Illumina MiSeq platform to identify bacterial taxa, and GIS to measure vegetation cover in buffer zones of different diameters. Our goal was to explore variation among highly vegetated (parks) versus non-vegetated (parking lots) urban environments. A secondary objective was to evaluate passive versus active collection methods for outdoor airborne microbial sampling. Airborne bacterial communities from five parks were different from those of five parking lots (p=0.023), although alpha diversity was similar. Direct gradient analysis showed that the proportion of vegetated area within a 50m radius of the sampling station explained 15% of the variation in bacterial community composition. A number of key taxa, including several Acidobacteriaceae were substantially more abundant in parks, while parking lots had higher relative abundance of Acetobacteraceae. Parks had greater beta diversity than parking lots, i.e. individual parks were characterized by unique bacterial signatures, whereas parking lot communities tended to be similar to each other. Although parks and parking lots were selected to form pairs of nearby sites, spatial proximity did not appear to affect compositional similarity. Our results also showed that passive and active collection methods gave comparable results, indicating the "settling dish" method is effective for outdoor airborne sampling. This work sets a foundation for understanding how urban vegetation may impact microbial communities, with potential implications for designing neighborhoods and open space systems that foster better human health.
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Affiliation(s)
- Gwynne Mhuireach
- Department of Landscape Architecture, University of Oregon, Eugene, OR, United States; Institute for a Sustainable Environment, University of Oregon, Eugene, OR, United States; Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States; Energy Studies in Buildings Laboratory, Department of Architecture, University of Oregon, Eugene, OR, United States.
| | - Bart R Johnson
- Department of Landscape Architecture, University of Oregon, Eugene, OR, United States; Institute for a Sustainable Environment, University of Oregon, Eugene, OR, United States
| | - Adam E Altrichter
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Joshua Ladau
- Gladstone Institutes, University of California, San Francisco, CA, United States
| | - James F Meadow
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Katherine S Pollard
- Gladstone Institutes, University of California, San Francisco, CA, United States; Division of Biostatistics, Institute for Human Genetics, Institute for Computational Health Sciences, University of California, San Francisco, CA 94158, United States
| | - Jessica L Green
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
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Fort T, Robin C, Capdevielle X, Delière L, Vacher C. Foliar fungal communities strongly differ between habitat patches in a landscape mosaic. PeerJ 2016; 4:e2656. [PMID: 27833817 PMCID: PMC5101609 DOI: 10.7717/peerj.2656] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/05/2016] [Indexed: 11/28/2022] Open
Abstract
Background Dispersal events between habitat patches in a landscape mosaic can structure ecological communities and influence the functioning of agrosystems. Here we investigated whether short-distance dispersal events between vineyard and forest patches shape foliar fungal communities. We hypothesized that these communities homogenize between habitats over the course of the growing season, particularly along habitat edges, because of aerial dispersal of spores. Methods We monitored the richness and composition of foliar and airborne fungal communities over the season, along transects perpendicular to edges between vineyard and forest patches, using Illumina sequencing of the Internal Transcribed Spacer 2 (ITS2) region. Results In contrast to our expectation, foliar fungal communities in vineyards and forest patches increasingly differentiate over the growing season, even along habitat edges. Moreover, the richness of foliar fungal communities in grapevine drastically decreased over the growing season, in contrast to that of forest trees. The composition of airborne communities did not differ between habitats. The composition of oak foliar fungal communities change between forest edge and centre. Discussion These results suggest that dispersal events between habitat patches are not major drivers of foliar fungal communities at the landscape scale. Selective pressures exerted in each habitat by the host plant, the microclimate and the agricultural practices play a greater role, and might account for the differentiation of foliar fugal communities between habitats.
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Affiliation(s)
- Thomas Fort
- BIOGECO, UMR 1202, INRA, Université de Bordeaux , Cestas , France
| | - Cécile Robin
- BIOGECO, UMR 1202, INRA, Université de Bordeaux , Cestas , France
| | | | - Laurent Delière
- SAVE, UMR 1065, INRA, ISVV, Université de Bordeaux , Villenave d'Ornon , France
| | - Corinne Vacher
- BIOGECO, UMR 1202, INRA, Université de Bordeaux , Pessac , France
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Vacher C, Hampe A, Porté AJ, Sauer U, Compant S, Morris CE. The Phyllosphere: Microbial Jungle at the Plant–Climate Interface. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032238] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Arndt Hampe
- BIOGECO, INRA, Univ. Bordeaux, 33610 Cestas, France
| | | | - Ursula Sauer
- Bioresources Unit, Department of Health and Environment, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria
| | - Stéphane Compant
- Bioresources Unit, Department of Health and Environment, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria
| | - Cindy E. Morris
- INRA, Unité de Recherche de Pathologie Végétale, 84143 Montfavet, France
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Meaden S, Metcalf CJE, Koskella B. The effects of host age and spatial location on bacterial community composition in the English Oak tree (Quercus robur). ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:649-658. [PMID: 27120417 DOI: 10.1111/1758-2229.12418] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 04/08/2016] [Indexed: 06/05/2023]
Abstract
Drivers of bacterial community assemblages associated with plants are diverse and include biotic factors, such as competitors and host traits, and abiotic factors, including environmental conditions and dispersal mechanisms. We examine the roles of spatial distribution and host size, as an approximation for age, in shaping the microbiome associated with Quercus robur woody tissue using culture-independent 16S rRNA gene amplicon sequencing. In addition to providing a baseline survey of the Q. robur microbiome, we screened for the pathogen of acute oak decline. Our results suggest that age is a predictor of bacterial community composition, demonstrating a surprising negative correlation between tree age and alpha diversity. We find no signature of dispersal limitation within the Wytham Woods plot sampled. Together, these results provide evidence for niche-based hypotheses of community assembly and the importance of tree age in bacterial community structure, as well as highlighting that caution must be applied when diagnosing dysbiosis in a long-lived plant host.
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Affiliation(s)
- S Meaden
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, TR109FE, United Kingdom
| | - C J E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA
- Fogarty International Center, National Institute of Health, Bethesda, Maryland, USA
| | - B Koskella
- Department of Integrative Biology, University of California, Berkeley, 94720, USA
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Laforest-Lapointe I, Messier C, Kembel SW. Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species. PeerJ 2016; 4:e2367. [PMID: 27635335 PMCID: PMC5012278 DOI: 10.7717/peerj.2367] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 07/25/2016] [Indexed: 11/20/2022] Open
Abstract
Background The diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada. Methods We targeted five dominant temperate forest tree species including angiosperms and gymnosperms: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea and Picea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height), the four cardinal points of mid-canopy (2–4 m height), and the top-canopy (4–6 m height). We also collected bottom-canopy leaves from five additional trees from each species. Results Based on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%). Discussion Our results suggest that individual samples from consistent positions within the tree canopy from multiple individuals per species can be used to accurately quantify variation in phyllosphere bacterial community structure. However, the considerable amount of intra-individual variation within a tree canopy ask for a better understanding of how changes in leaf characteristics and local abiotic conditions drive spatial variation in the phyllosphere microbiome.
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Affiliation(s)
- Isabelle Laforest-Lapointe
- Centre d'étude de la forêt, Montreal, Canada; Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec, Canada
| | - Christian Messier
- Centre d'étude de la forêt, Montreal, Canada; Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec, Canada; ISFORT - Institut des Sciences de la Forêt Tempérée, Université du Québec en Outaouais, Ripon, Quebec, Canada
| | - Steven W Kembel
- Centre d'étude de la forêt, Montreal, Canada; Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec, Canada
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Biodiversity, the Human Microbiome and Mental Health: Moving toward a New Clinical Ecology for the 21st Century? ACTA ACUST UNITED AC 2016. [DOI: 10.1155/2016/2718275] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Advances in research concerning the brain-related influences of the microbiome have been paradigm shifting, although at an early stage, clinical research involving beneficial microbes lends credence to the notion that the microbiome may be an important target in supporting mental health (defined here along the continuum between quality of life and the criteria for specific disorders). Through metagenomics, proteomics, metabolomics, and systems biology, a new emphasis to personalized medicine is on the horizon. Humans can now be viewed as multispecies organisms operating within an ecological theatre; it is important that clinicians increasingly see their patients in this context. Historically marginalized ecological aspects of health are destined to become an important consideration in the new frontiers of practicing medicine with the microbiome in mind. Emerging evidence indicates that macrobiodiversity in the external environment can influence mental well-being. Local biodiversity may also drive differences in human-associated microbiota; microbial diversity as a product of external biodiversity may have far-reaching effects on immune function and mood. With a focus on the microbiome as it pertains to mental health, we define environmental “grey space” and emphasize a new frontier involving bio-eco-psychological medicine. Within this concept the ecological terrain can link dysbiotic lifestyles and biodiversity on the grand scale to the local human-associated microbial ecosystems that might otherwise seem far removed from one another.
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Rigonato J, Gonçalves N, Andreote APD, Lambais MR, Fiore MF. Estimating genetic structure and diversity of cyanobacterial communities in Atlantic forest phyllosphere. Can J Microbiol 2016; 62:953-960. [PMID: 27696898 DOI: 10.1139/cjm-2016-0229] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cyanobacterial communities on the phyllosphere of 4 plant species inhabiting the endangered Brazilian Atlantic Forest biome were evaluated using cultivation-independent molecular approaches. Total genomic DNA was extracted from cells detached from the surface of leaves of Euterpe edulis, Guapira opposita, Garcinia gardneriana, and Merostachys neesii sampled in 2 Brazilian Atlantic Forest locations along an elevational gradient, i.e., lowland and montane forest. The DNA fingerprinting method PCR-DGGE revealed that the cyanobacterial phyllosphere community structures were mainly influenced by the plant species; geographical location of the plant had little effect. The 16S rRNA gene sequences obtained by clone libraries showed a predominance of nitrogen-fixing cyanobacteria of the order Nostocales, even though the majority of retrieved operational taxonomic units (∼60% of the sequences) showed similarity only to uncultured cyanobacteria phylotypes. The leaf surface of Guapira opposita had the highest richness and diversity of cyanobacteria, whereas the M. neesii (bamboo) had the largest number of copies of cyanobacterial 16S rRNA gene per cm2 of leaf. This study investigated cyanobacteria diversity and its distribution pattern in Atlantic forest phyllosphere. The results indicated that plant species is the main driver of cyanobacteria community assemblage in the phyllosphere and that these communities are made up of a high diversity of cyanobacterial taxa that need to be discovered.
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Affiliation(s)
- Janaina Rigonato
- a University of São Paulo, Center for Nuclear Energy in Agriculture, CENA/USP, Piracicaba-SP, Brazil
| | - Natalia Gonçalves
- a University of São Paulo, Center for Nuclear Energy in Agriculture, CENA/USP, Piracicaba-SP, Brazil
| | - Ana Paula Dini Andreote
- a University of São Paulo, Center for Nuclear Energy in Agriculture, CENA/USP, Piracicaba-SP, Brazil
| | | | - Marli Fátima Fiore
- a University of São Paulo, Center for Nuclear Energy in Agriculture, CENA/USP, Piracicaba-SP, Brazil
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47
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Laforest-Lapointe I, Messier C, Kembel SW. Host species identity, site and time drive temperate tree phyllosphere bacterial community structure. MICROBIOME 2016; 4:27. [PMID: 27316353 PMCID: PMC4912770 DOI: 10.1186/s40168-016-0174-1] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/24/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND The increasing awareness of the role of phyllosphere microbial communities in plant health calls for a greater understanding of their structure and dynamics in natural ecosystems. Since most knowledge of tree phyllosphere bacterial communities has been gathered in tropical forests, our goal was to characterize the community structure and assembly dynamics of phyllosphere epiphytic bacterial communities in temperate forests in Quebec, Canada. We targeted five dominant tree species: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea, and Picea glauca. We collected 180 samples of phyllosphere communities on these species at four natural forest sites, three times during the growing season. RESULTS Host functional traits (i.e., wood density, leaf nitrogen content) and climate variables (summer mean temperature and precipitation) were strongly correlated with community structure. We highlight three key findings: (1) temperate tree species share a "core microbiome"; (2) significant evolutionary associations exist between groups of bacteria and host species; and (3) a greater part of the variation in phyllosphere bacterial community assembly is explained by host species identity (27 %) and species-site interaction (14 %), than by site (11 %) or time (1 %). CONCLUSIONS We demonstrated that host species identity is a stronger driver of temperate tree phyllosphere bacterial communities than site or time. Our results suggest avenues for future studies on the influence of host functional traits on phyllosphere community functional biogeography across terrestrial biomes.
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Affiliation(s)
- Isabelle Laforest-Lapointe
- Département des sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, H3C 3P8, Québec, Canada.
- Centre d'étude de la forêt, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, H3C 3P8, Québec, Canada.
| | - Christian Messier
- Département des sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, H3C 3P8, Québec, Canada
- Centre d'étude de la forêt, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, H3C 3P8, Québec, Canada
- Institut des Sciences de la Forêt tempérée, Université du Québec en Outaouais, Ripon, J0V 1V0, Québec, Canada
| | - Steven W Kembel
- Département des sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, H3C 3P8, Québec, Canada
- Centre d'étude de la forêt, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, H3C 3P8, Québec, Canada
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48
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Islam MS, Zhang Y, McPhedran KN, Liu Y, Gamal El-Din M. Mechanistic investigation of industrial wastewater naphthenic acids removal using granular activated carbon (GAC) biofilm based processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 541:238-246. [PMID: 26410699 DOI: 10.1016/j.scitotenv.2015.09.091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/16/2015] [Accepted: 09/17/2015] [Indexed: 06/05/2023]
Abstract
Naphthenic acids (NAs) found in oil sands process-affected waters (OSPW) have known environmental toxicity and are resistant to conventional wastewater treatments. The granular activated carbon (GAC) biofilm treatment process has been shown to effectively treat OSPW NAs via combined adsorption/biodegradation processes despite the lack of research investigating their individual contributions. Presently, the NAs removals due to the individual processes of adsorption and biodegradation in OSPW bioreactors were determined using sodium azide to inhibit biodegradation. For raw OSPW, after 28 days biodegradation and adsorption contributed 14% and 63% of NA removal, respectively. For ozonated OSPW, biodegradation removed 18% of NAs while adsorption reduced NAs by 73%. Microbial community 454-pyrosequencing of bioreactor matrices indicated the importance of biodegradation given the diverse carbon degrading families including Acidobacteriaceae, Ectothiorhodospiraceae, and Comamonadaceae. Overall, results highlight the ability to determine specific processes of NAs removals in the combined treatment process in the presence of diverse bacteria metabolic groups found in GAC bioreactors.
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Affiliation(s)
- Md Shahinoor Islam
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 2W2, Canada; Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
| | - Yanyan Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 2W2, Canada
| | - Kerry N McPhedran
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 2W2, Canada; Department of Civil and Geological Engineering, College of Engineering, University of Saskatchewan, Saskatoon S7N 5A9, Canada
| | - Yang Liu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 2W2, Canada.
| | - Mohamed Gamal El-Din
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 2W2, Canada.
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Craig JM, Logan AC, Prescott SL. Natural environments, nature relatedness and the ecological theater: connecting satellites and sequencing to shinrin-yoku. J Physiol Anthropol 2016; 35:1. [PMID: 26763049 PMCID: PMC4712592 DOI: 10.1186/s40101-016-0083-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/07/2016] [Indexed: 02/08/2023] Open
Abstract
Recent advances in research concerning the public health value of natural environments have been remarkable. The growing interest in this topic (often housed under terms such as green and/or blue space) has been occurring in parallel with the microbiome revolution and an increased use of remote sensing technology in public health. In the context of biodiversity loss, rapid urbanization, and alarming rates of global non-communicable diseases (many associated with chronic, low-grade inflammation), discussions of natural vis-a-vis built environments are not merely fodder for intellectual curiosity. Here, we argue for increased interdisciplinary collaboration with the aim of better understanding the mechanisms—including aerobiological and epigenetic—that might help explain some of the noted positive health outcomes. It is our contention that some of these mechanisms are related to ecodiversity (i.e., the sum of biodiversity and geodiversity, including biotic and abiotic constituents). We also encourage researchers to more closely examine individual nature relatedness and how it might influence many outcomes that are at the interface of lifestyle habits and contact with ecodiversity.
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Affiliation(s)
- Jeffrey M Craig
- Murdoch Childrens Research Institute; Department of Paediatrics, University of Melbourne, The Royal Children's Hospital, Flemington Road, Parkville, Victoria, 3052, Australia. .,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN), Perth, Australia.
| | - Alan C Logan
- CAMNR, 23679 Calabassas Road, Suite 542, Calabassas, CA, 91302, USA. .,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN), Perth, Australia.
| | - Susan L Prescott
- School of Paediatrics and Child Health, Princess Margaret Hospital for Children, University of Western Australia, GPO Box D 184, Perth, WA, 6840, Australia. .,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN), Perth, Australia.
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Van Stan JT, Pypker TG. A review and evaluation of forest canopy epiphyte roles in the partitioning and chemical alteration of precipitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 536:813-824. [PMID: 26254081 DOI: 10.1016/j.scitotenv.2015.07.134] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/24/2015] [Accepted: 07/27/2015] [Indexed: 05/26/2023]
Abstract
Interactions between precipitation and forest canopy elements (bark, leaves, and epiphytes) control the quantity, spatiotemporal patterning, and the chemical concentration, character and constituency of precipitation to soils. Canopy epiphytes exert a range of hydrological and biogeochemical effects due to their diversity of morphological traits and nutrient acquisition mechanisms. We reviewed and evaluated the state of knowledge regarding epiphyte interactions with precipitation partitioning (into interception loss, throughfall, and stemflow) and the chemical alteration of net precipitation fluxes (throughfall and stemflow). As epiphyte species are quite diverse, this review categorized findings by common paraphyletic groups: lichens, bryophytes, and vascular epiphytes. Of these groups, vascular epiphytes have received the least attention and lichens the most. In general, epiphytes decrease throughfall and stemflow and increase interception loss. Epiphytes alter the spatiotemporal pattern of throughfall and increase overall latent heat fluxes from the canopy. Epiphytes alter biogeochemical processes by impacting the transfer of solutes through the canopy; however, the change in solute concentration varies with epiphyte type and chemical species. We discuss several important knowledge gaps across all epiphyte groups. We also explore innovative methods that currently exist to confront these knowledge gaps and past techniques applied to gain our current understanding. Future research addressing the listed deficiencies will improve our knowledge of epiphyte roles in water and biogeochemical processes coupled within forest canopies-processes crucial to supporting microbe, plant, vertebrate and invertebrate communities within individual epiphytes, epiphyte assemblages, host trees, and even the forest ecosystem as a whole.
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Affiliation(s)
- John T Van Stan
- Dept. of Geology and Geography, Georgia Southern University, Statesboro, GA 30460, USA.
| | - Thomas G Pypker
- Dept. of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
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