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Iqbal MM, Nishimura M, Tsukamoto Y, Yoshizawa S. Changes in microbial community structure related to biodegradation of eelgrass (Zostera marina). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172798. [PMID: 38688366 DOI: 10.1016/j.scitotenv.2024.172798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/21/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Seagrass meadows produce organic carbon and deposit it on the seabed through the decaying process. Microbial activity is closely related to the process of eelgrass death and collapse. We investigated the microbial community structure of eelgrass during the eelgrass decomposition process by using a microcosm containing raw seawater and excised eelgrass leaves collected from a Zostera marina bed in Futtsu, Chiba Prefecture, Japan. The fast-growing microbes (i.e., Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia) rapidly adhered to the eelgrass leaf surface and proliferated in the first two weeks but gradually decreased the relative abundance as the months moved on. On the other hand, the slow-growing microbes (i.e., Cytophagia, Anaerolineae, Thaumarchaeota, and Actinobacteria) became predominant over the eelgrass surface late in the culture experiment (120, 180 days). The fast-growing groups of Gammaproteobacteria and Flavobacteriia appear to be closely related to the initial decomposition of eelgrass, especially the rapid decomposition of leaf-derived biopolymers. Changes in nitrogen content due to the bacterial rapid consumption of readily degradable organic carbon induced changes in the community structure at the early stage of eelgrass decomposition. In addition, shifts in the C/N ratio were driven by microbial community changes during later decomposition phases.
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Affiliation(s)
- Md Mehedi Iqbal
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8563, Japan.
| | - Masahiko Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Yuya Tsukamoto
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8563, Japan.
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Huang L, Fu Y, Liu Y, Chen Y, Wang T, Wang M, Lin X, Feng Y. Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172231. [PMID: 38608902 DOI: 10.1016/j.scitotenv.2024.172231] [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: 10/23/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.
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Affiliation(s)
- Lukuan Huang
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingyi Fu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yaru Liu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yijie Chen
- IDEO Play Lab, CA 91006, United States of America
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Meixia Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Xianyong Lin
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Feng
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Ayilara MS, Adeleke BS, Babalola OO. Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria. MICROBIAL ECOLOGY 2023; 85:1113-1135. [PMID: 36319743 PMCID: PMC10156819 DOI: 10.1007/s00248-022-02136-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/24/2022] [Indexed: 05/04/2023]
Abstract
This review evaluates oilseed crop soybean endophytic bacteria, their prospects, and challenges for sustainable agriculture. Soybean is one of the most important oilseed crops with about 20-25% protein content and 20% edible oil production. The ability of soybean root-associated microbes to restore soil nutrients enhances crop yield. Naturally, the soybean root endosphere harbors root nodule bacteria, and endophytic bacteria, which help increase the nitrogen pool and reclamation of another nutrient loss in the soil for plant nutrition. Endophytic bacteria can sustain plant growth and health by exhibiting antibiosis against phytopathogens, production of enzymes, phytohormone biosynthesis, organic acids, and secondary metabolite secretions. Considerable effort in the agricultural industry is focused on multifunctional concepts and bioprospecting on the use of bioinput from endophytic microbes to ensure a stable ecosystem. Bioprospecting in the case of this review is a systemic overview of the biorational approach to harness beneficial plant-associated microbes to ensure food security in the future. Progress in this endeavor is limited by available techniques. The use of molecular techniques in unraveling the functions of soybean endophytic bacteria can explore their use in integrated organic farming. Our review brings to light the endophytic microbial dynamics of soybeans and current status of plant microbiome research for sustainable agriculture.
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Affiliation(s)
- Modupe Stella Ayilara
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| | - Bartholomew Saanu Adeleke
- Department of Biological Sciences, Microbiology Unit, Faculty of Science, Olusegun Agagu University of Science and Technology, PMB 353, Okitipupa, Nigeria
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
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Posidonia oceanica (L.) Delile: A Mediterranean seagrass with potential applications but regularly and erroneously referred to as an algal species. Int J Biol Macromol 2023; 230:122624. [PMID: 36403775 DOI: 10.1016/j.ijbiomac.2022.11.169] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Posidonia oceanica (L.) Delile is one of the most abundant aquatic vascular higher plants in the Mediterranean Sea belonging to Posidoniaceas family. It is considered as a valuable natural source for multiple uses either for ecological functions or industrial applications. Nevertheless, this marine phanerogam is commonly confused with macroalgae, or seaweeds, known also as cryptogams. The present note intends to discuss the mis-use of the associated terminology of P. oceanica as algae in the scientific literature in order to avoid the widespread of this issue in the future. Thus, an extensive assessment of some important published woks has been conducted. This note will certainly allow the accurate nomenclature of this promising endemic species, which will continue its valorizations' ascension in several potential applications.
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Conte C, Apostolaki ET, Vizzini S, Migliore L. A Tight Interaction between the Native Seagrass Cymodocea nodosa and the Exotic Halophila stipulacea in the Aegean Sea Highlights Seagrass Holobiont Variations. PLANTS (BASEL, SWITZERLAND) 2023; 12:350. [PMID: 36679063 PMCID: PMC9863530 DOI: 10.3390/plants12020350] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Seagrasses harbour bacterial communities with which they constitute a functional unit called holobiont that responds as a whole to environmental changes. Epiphytic bacterial communities rapidly respond to both biotic and abiotic factors, potentially contributing to the host fitness. The Lessepsian migrant Halophila stipulacea has a high phenotypical plasticity and harbours a highly diverse epiphytic bacterial community, which could support its invasiveness in the Mediterranean Sea. The current study aimed to evaluate the Halophila/Cymodocea competition in the Aegean Sea by analysing each of the two seagrasses in a meadow zone where these intermingled, as well as in their monospecific zones, at two depths. Differences in holobionts were evaluated using seagrass descriptors (morphometric, biochemical, elemental, and isotopic composition) to assess host changes, and 16S rRNA gene to identify bacterial community structure and composition. An Indicator Species Index was used to identify bacteria significantly associated with each host. In mixed meadows, native C. nodosa was shown to be affected by the presence of exotic H. stipulacea, in terms of both plant descriptors and bacterial communities, while H. stipulacea responded only to environmental factors rather than C. nodosa proximity. This study provided evidence of the competitive advantage of H. stipulacea on C. nodosa in the Aegean Sea and suggests the possible use of associated bacterial communities as an ecological seagrass descriptor.
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Affiliation(s)
- Chiara Conte
- PhD Program in Evolutionary Biology and Ecology, University of Rome Tor Vergata, 00133 Rome, Italy
- Laboratory of Ecology and Ecotoxicology, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Eugenia T. Apostolaki
- Institute of Oceanography, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Salvatrice Vizzini
- Department of Earth and Marine Sciences, University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
- CoNISMa, National Interuniversity Consortium for Marine Sciences, Piazzale Flaminio 9, 00196 Roma, Italy
| | - Luciana Migliore
- Laboratory of Ecology and Ecotoxicology, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- eCampus University, Via Isimbardi 10, 22060 Novedrate (CO), Italy
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Kandasamy GD, Kathirvel P. Insights into bacterial endophytic diversity and isolation with a focus on their potential applications –A review. Microbiol Res 2022; 266:127256. [DOI: 10.1016/j.micres.2022.127256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 11/02/2022] [Accepted: 11/06/2022] [Indexed: 11/14/2022]
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7
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Pan Y, Li G, Su L, Zheng P, Wang Y, Shen Z, Chen Z, Han Q, Gong J. Seagrass Colonization Alters Diversity, Abundance, Taxonomic, and Functional Community Structure of Benthic Microbial Eukaryotes. Front Microbiol 2022; 13:901741. [PMID: 35770161 PMCID: PMC9234489 DOI: 10.3389/fmicb.2022.901741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/03/2022] [Indexed: 11/26/2022] Open
Abstract
Seagrass form high productive ecosystems in coastal environments. However, the effects of these coastal plants on the structure and function of the belowground eukaryotic microbiome remain elusive. In this study, we characterized the community of microbial eukaryotes (microeukaryotes) in both vegetated and unvegetated sediments using 18S rRNA gene amplicon sequencing and quantitative PCR. Analysis of sequencing data showed that the eelgrass (Zostera marina) colonization decreased the alpha diversity indices of benthic microeukaryotes. Apicomplexa represented an average of 83% of reads across all samples, with a higher proportion at the vegetated sites. The taxonomic community structure was significantly different between these two types of sediments, for which the concentration ofNH 4 + in sediment porewater and salinity could account. Phylogenetic analyses of long 18S rRNA genes (around 1,030 bp) indicated these apicomplexan parasites are closely related to gregarine Lecudina polymorpha. Determination of 18S rRNA gene abundances provided evidence that the eelgrass markedly promoted the biomass of the gregarine and all microeukaryotes in the seagrass-colonized sediments and confirmed that the gregarine was hosted by a polychaete species. Significantly higher gene abundances of heterotrophs and mixotrophs were found at the vegetated sites, which could be explained by the finer sediments and short supply of dissolved inorganic nitrogen, respectively. The pigmented protists were more abundant in 18S rRNA gene copies at the lower and higher pH levels than at the intermediate. Nevertheless, the fractions of heterotrophs and phototrophs in the community were significantly related to porewater N:P ratio. These results indicate that seagrass colonization significantly induces an increase in overall biomass and a decrease in diversity of benthic microeukaryotes, making them more heterotrophic. This study also highlights that the hotspot of eukaryotic parasites could be linked with the high productivity of a natural ecosystem.
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Affiliation(s)
- Ying Pan
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Guihao Li
- Laboratory of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Lei Su
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Pengfei Zheng
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Yaping Wang
- Laboratory of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Zhuo Shen
- Laboratory of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Qiuying Han
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, China
| | - Jun Gong
- Laboratory of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
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8
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Cultivable Fungal Endophytes in Roots, Rhizomes and Leaves of Posidonia oceanica (L.) Delile along the Coast of Sicily, Italy. PLANTS 2022; 11:plants11091139. [PMID: 35567139 PMCID: PMC9105210 DOI: 10.3390/plants11091139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022]
Abstract
The presence of endophytic fungi in the roots, rhizomes, and leaves of Posidonia oceanica was evaluated in different localities of the Sicilian coast. Samples of roots, rhizomes, and leaves were submitted to isolation techniques, and the obtained fungal colonies were identified by morphological and molecular (rRNA sequencing) analysis. Fungal endophytes occurred mainly in roots and occasionally in rhizomes and leaves. Lulwoana sp. was the most frequent of the isolated taxa, suggesting a strong interaction with the host. In addition, eight other fungal taxa were isolated. In particular, fungi of the genus Ochroconis and family Xylariaceae were identified as endophytes in healthy plants at all sampling stations, whereas Penicillium glabrum was isolated at only one sampling station. Thus, several organs, especially roots of Posidonia oceanica, harbor endophytic fungi, potentially involved in supporting the living host as ascertained for terrestrial plants.
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9
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Multidrug-resistant epi-endophytic bacterial community in Posidonia oceanica of Mahdia coast as biomonitoring factor for antibiotic contamination. Arch Microbiol 2022; 204:229. [PMID: 35353264 DOI: 10.1007/s00203-022-02842-9] [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: 12/17/2021] [Revised: 03/12/2022] [Accepted: 03/13/2022] [Indexed: 11/02/2022]
Abstract
Faced with the significant disturbances, mainly of anthropogenic origin, which affect the Mediterranean coastal ecosystem, Posidonia oceanica (L.) Delile has often been used to assess the state of health of this environment. The present study aims to determine the multidrug resistance patterns among isolated and identified epi-endophytic bacterial strains in P. oceanica seagrass collected from Mahdia coastal seawater (Tunisia). To investigate the bacterial community structure and diversity from coastal seawater samples from Mahdia, total DNA extraction and 16S rRNA gene amplification were performed and analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE profiles showed that some bands were specific to a given site, while other bands were found to be common to more than one sample. In the other hand, bacterial strains were isolated from 1 mL of leaves and epiphytes suspension of P. oceanica seagrass in marine agar. Forty-three isolates were obtained, seven of them were selected and identified on the basis of 16S rRNA gene sequence analysis. These isolates belonged to the genus Bacillus, exhibiting 98-100% of identity with known sequences. Susceptibility patterns of these strains were studied toward commonly used antibiotics in Tunisia. All identified isolates were resistant to Aztreonam (72.1%), Ceftazidime (60.5%), Amoxicillin (56%) and Rifampicin (51.2%). S5-L13 strain had presented the highest multidrug resistance with a MAR index of 0.67.
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10
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Tarquinio F, Attlan O, Vanderklift MA, Berry O, Bissett A. Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds. Front Microbiol 2021; 12:703014. [PMID: 34621247 PMCID: PMC8491609 DOI: 10.3389/fmicb.2021.703014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.
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Affiliation(s)
- Flavia Tarquinio
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Océane Attlan
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Sciences et Technologies, Université de la Réunion, Saint-Denis, France
| | - Mathew A Vanderklift
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
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11
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Dutta S, Na CS, Lee YH. Features of Bacterial Microbiota in the Wild Habitat of Pulsatilla tongkangensis, the Endangered "Long-Sepal Donggang Pasque-Flower Plant," Endemic to Karst Topography of Korea. Front Microbiol 2021; 12:656105. [PMID: 34305828 PMCID: PMC8297415 DOI: 10.3389/fmicb.2021.656105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/14/2021] [Indexed: 12/26/2022] Open
Abstract
Microbes associated with plants significantly influence the development and health of the plants. The diversity and function of microbiomes associated with the long-sepal Donggang pasque-flower (DPF) plant, an endemic and endangered species in karst ecosystems, remain unexplored. In this study, we investigated the features of bacterial communities associated with the rhizosphere and roots of DPF plants and their functions in plant growth promotion. The DPF plants were collected from natural and cultivated habitats, and their 16S rDNA was sequenced to assess the bacterial community structures. The bacterial microbiota was more diverse in wild than in cultivated plants. The core bacterial microbiota commonly functioned as endophytes in both wild and cultivated DPF plants, although there were some differences. The identified bacterial strains benefited plants through nitrogen fixation, phosphate solubilization, or phytohormone production, inducing measurable growth differences in Arabidopsis thaliana. To the best of our knowledge, this study is the first to report the bacterial community structures associated with the rhizosphere soil and roots of DPF plants in karst ecosystems. The bacterial strains isolated in this study could be used to aid sustainable growth and restoration of rare plants in karst ecosystems. Our systematic research on the microbiomes associated with these endangered plants will contribute to their conservation as well as development of better cultivation.
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Affiliation(s)
- Swarnalee Dutta
- Division of Biotechnology, Jeonbuk National University, Iksan, South Korea
| | - Chae Sun Na
- Seed Viability Research Team, Baekdudaegan National Arboretum, Bonghwa-gun, South Korea
| | - Yong Hoon Lee
- Division of Biotechnology, Jeonbuk National University, Iksan, South Korea.,Plant Medical Research Center, Advanced Institute of Environment and Bioscience, and Institute of Bio-industry, Jeonbuk National University, Jeonju, South Korea
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12
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The Seagrass Holobiont: What We Know and What We Still Need to Disclose for Its Possible Use as an Ecological Indicator. WATER 2021. [DOI: 10.3390/w13040406] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Microbes and seagrass establish symbiotic relationships constituting a functional unit called the holobiont that reacts as a whole to environmental changes. Recent studies have shown that the seagrass microbial associated community varies according to host species, environmental conditions and the host’s health status, suggesting that the microbial communities respond rapidly to environmental disturbances and changes. These changes, dynamics of which are still far from being clear, could represent a sensitive monitoring tool and ecological indicator to detect early stages of seagrass stress. In this review, the state of art on seagrass holobiont is discussed in this perspective, with the aim of disentangling the influence of different factors in shaping it. As an example, we expand on the widely studied Halophila stipulacea’s associated microbial community, highlighting the changing and the constant components of the associated microbes, in different environmental conditions. These studies represent a pivotal contribution to understanding the holobiont’s dynamics and variability pattern, and to the potential development of ecological/ecotoxicological indices. The influences of the host’s physiological and environmental status in changing the seagrass holobiont, alongside the bioinformatic tools for data analysis, are key topics that need to be deepened, in order to use the seagrass-microbial interactions as a source of ecological information.
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13
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Garcias-Bonet N, Eguíluz VM, Díaz-Rúa R, Duarte CM. Host-association as major driver of microbiome structure and composition in Red Sea seagrass ecosystems. Environ Microbiol 2020; 23:2021-2034. [PMID: 33225561 DOI: 10.1111/1462-2920.15334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
The role of the microbiome in sustaining seagrasses has recently been highlighted. However, our understanding of the seagrass microbiome lacks behind that of other organisms. Here, we analyse the endophytic and total bacterial communities of leaves, rhizomes, and roots of six Red Sea seagrass species and their sediments. The structure of seagrass bacterial communities revealed that the 1% most abundant OTUs accounted for 87.9% and 74.8% of the total numbers of reads in sediment and plant tissue samples, respectively. We found taxonomically distinct bacterial communities in vegetated and bare sediments. Yet, our results suggest that lifestyle (i.e. free-living or host-association) is the main driver of bacterial community composition. Seagrass bacterial communities were tissue- and species-specific and differed from those of surrounding sediments. We identified OTUs belonging to genera related to N and S cycles in roots, and members of Actinobacteria, Bacteroidetes, and Firmicutes phyla as particularly enriched in root endosphere. The finding of highly similar OTUs in well-defined sub-clusters by network analysis suggests the co-occurrence of highly connected key members within Red Sea seagrass bacterial communities. These results provide key information towards the understanding of the role of microorganisms in seagrass ecosystem functioning framed under the seagrass holobiont concept.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Víctor M Eguíluz
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.,Instituto de Física Interdisciplinar y Sistemas Complejos (CSIC-UIB), Palma de Mallorca, E-07122, Spain
| | - Rubén Díaz-Rúa
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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Kohn T, Rast P, Kallscheuer N, Wiegand S, Boedeker C, Jetten MSM, Jeske O, Vollmers J, Kaster AK, Rohde M, Jogler M, Jogler C. The Microbiome of Posidonia oceanica Seagrass Leaves Can Be Dominated by Planctomycetes. Front Microbiol 2020; 11:1458. [PMID: 32754127 PMCID: PMC7366357 DOI: 10.3389/fmicb.2020.01458] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
Seagrass meadows are ubiquitous, fragile and endangered marine habitats, which serve as fish breeding grounds, stabilize ocean floor substrates, retain nutrients and serve as important carbon sinks, counteracting climate change. In the Mediterranean Sea, seagrass meadows are mostly formed by the slow-growing endemic plant Posidonia oceanica (Neptune grass), which is endangered by global warming and recreational motorboating. Despite its importance, surprisingly little is known about the leaf surface microbiome of P. oceanica. Using amplicon sequencing, we here show that species belonging to the phylum Planctomycetes can dominate the biofilms of young and aged P. oceanica leaves. Application of selective cultivation techniques allowed for the isolation of two novel planctomycetal strains belonging to two yet uncharacterized genera.
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Affiliation(s)
- Timo Kohn
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Patrick Rast
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | | | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Christian Boedeker
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Mike S. M. Jetten
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Olga Jeske
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - John Vollmers
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
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15
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Kolátková V, Čepička I, Gargiulo GM, Vohník M. Enigmatic Phytomyxid Parasite of the Alien Seagrass Halophila stipulacea: New Insights into Its Ecology, Phylogeny, and Distribution in the Mediterranean Sea. MICROBIAL ECOLOGY 2020; 79:631-643. [PMID: 31664477 DOI: 10.1007/s00248-019-01450-3] [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: 07/04/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
Marine phytomyxids represent often overlooked obligate biotrophic parasites colonizing diatoms, brown algae, and seagrasses. An illustrative example of their enigmatic nature is the phytomyxid infecting the seagrass Halophila stipulacea (a well-known Lessepsian migrant from the Indo-Pacific to the Mediterranean Sea). In the Mediterranean, the occurrence of this phytomyxid was first described in 1995 in the Strait of Messina (southern Italy) and the second time in 2017 in the Aegean coast of Turkey. Here we investigated, using scuba diving, stereomicroscopy, light and scanning electron microscopy, and molecular methods, whether the symbiosis is still present in southern Italy, its distribution in this region and its relation to the previous reports. From the total of 16 localities investigated, the symbiosis has only been found at one site. A seasonal pattern was observed with exceptionally high abundance (> 40% of the leaf petioles colonized) in September 2017, absence of the symbiosis in May/June 2018, and then again high infection rates (~ 30%) in September 2018. In terms of anatomy and morphology as well as resting spore dimensions and arrangement, the symbiosis seems to be identical to the preceding observations in the Mediterranean. According to the phylogenetic analyses of the 18S rRNA gene, the phytomyxid represents the first characterized member of the environmental clade "TAGIRI-5". Our results provide new clues about its on-site ecology (incl. possible dispersal mechanisms), hint that it is rare but established in the Mediterranean, and encourage further research into its distribution, ecophysiology, and taxonomy.
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Affiliation(s)
- Viktorie Kolátková
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic.
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Gaetano Maurizio Gargiulo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Martin Vohník
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
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16
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Johnston‐Monje D, Lopez Mejia J. Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11334. [PMID: 32351795 PMCID: PMC7186905 DOI: 10.1002/aps3.11334] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/28/2020] [Indexed: 06/07/2023]
Abstract
High-throughput sequencing technologies have revolutionized the study of plant-associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant-associated microbiomes using molecular fingerprinting methodologies, including single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH-PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.
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Affiliation(s)
- David Johnston‐Monje
- Max Planck Tandem Group in Plant Microbial Ecology at the Universidad del ValleCalle 13 #100‐00, Building E20760032Cali, Valle del CaucaColombia
- Max Planck Institute for Plant Breeding ResearchDepartment of Plant Microbe InteractionsCarl-von-Linne-Weg 10D-50829CologneGermany
| | - Jessica Lopez Mejia
- Max Planck Tandem Group in Plant Microbial Ecology at the Universidad del ValleCalle 13 #100‐00, Building E20760032Cali, Valle del CaucaColombia
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17
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Tarquinio F, Hyndes GA, Laverock B, Koenders A, Säwström C. The seagrass holobiont: understanding seagrass-bacteria interactions and their role in seagrass ecosystem functioning. FEMS Microbiol Lett 2020; 366:5382495. [PMID: 30883643 DOI: 10.1093/femsle/fnz057] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 03/16/2019] [Indexed: 12/27/2022] Open
Abstract
This review shows that the presence of seagrass microbial community is critical for the development of seagrasses; from seed germination, through to phytohormone production and enhanced nutrient availability, and defence against pathogens and saprophytes. The tight seagrass-bacterial relationship highlighted in this review supports the existence of a seagrass holobiont and adds to the growing evidence for the importance of marine eukaryotic microorganisms in sustaining vital ecosystems. Incorporating a micro-scale view on seagrass ecosystems substantially expands our understanding of ecosystem functioning and may have significant implications for future seagrass management and mitigation against human disturbance.
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Affiliation(s)
- Flavia Tarquinio
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, Western Australia, Australia.,Commonwealth Scientific and Industrial Research Organization, Crawley, 6009, Western Australia, Australia
| | - Glenn A Hyndes
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Bonnie Laverock
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, 2007, Australia.,School of Science, Auckland University of Technology, Auckland, 1010, New Zealand
| | - Annette Koenders
- Centre for Ecosystem Management, Edith Cowan University, Joondalup, 6027, Western Australia, Australia
| | - Christin Säwström
- Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, Western Australia, Australia
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18
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Community Structure, Diversity and Potential of Endophytic Bacteria in the Primitive New Zealand Medicinal Plant Pseudowintera colorata. PLANTS 2020; 9:plants9020156. [PMID: 32012657 PMCID: PMC7076676 DOI: 10.3390/plants9020156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/15/2020] [Accepted: 01/23/2020] [Indexed: 12/12/2022]
Abstract
Although the importance of the plant microbiome in commercial plant health has been well established, there are limited studies in native medicinal plants. Pseudowintera colorata (horopito) is a native New Zealand medicinal plant recognized for its antimicrobial properties. Denaturing gradient gel electrophoresis (DGGE) and Illumina MiSeq analysis of P. colorata plants from ten sites across New Zealand showed that tissue type strongly influenced the diversity and richness of endophytic bacteria (PERMANOVA, P < 0.05). In addition, two OTUs belonging to the genus Pseudomonas (Greengenes ID: 646549 and 138914) were found to be present in >75% of all P. colorata leaf, stem and root samples and were identified as the members of the P. colorata “core endomicrobiome”. Culture-independent analysis was complemented by the recovery of 405 endophytic bacteria from the tissues of P. colorata. Some of these cultured endophytic bacteria (n = 10) showed high antagonism against four different phytopathogenic fungi tested. The influence of endophytic bacteria on plant growth was assessed by inoculating P. colorata seedlings. The mean shoot height of seedlings treated with Bacillus sp. TP1LA1B were longer (1.83×), had higher shoot dry weight (1.8×) and produced more internodes (1.8×) compared to the control.
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19
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Singh M, Ganguli S, Ghosh MM. Comparative metagenomic dataset of hospital effluent microbiome from rural and urban hospitals in West Bengal. Data Brief 2019; 25:104264. [PMID: 31440549 PMCID: PMC6699459 DOI: 10.1016/j.dib.2019.104264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/06/2019] [Accepted: 07/09/2019] [Indexed: 11/17/2022] Open
Abstract
The unsafe disposal of hospital effluents contributes to gross contamination of water bodies with antibiotic residues, antibiotic resistance genes and antibiotic resistance bacteria. This study reports the microbial community profile of hospital wastes collected from various regions of West Bengal, India, using 16S rRNA gene amplicon sequencing. The data set Liquid Sludge (LS) contains 15,372,973 reads with an average length of 301 bps with average 52 ± 5% GC content. The data set Solid Sludge (SS) contains 16,071,594 reads with an average length of 301 bps with average 53 ± 4% GC content. Data of this study are available at NCBI BioProject (PRJNA360379). In sample LS, an abundance of 19.3% for the members of Bacteroidetes was observed. In sample SS, an abundance of 19.7% for the members of Euryarchaeota was observed.
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Affiliation(s)
- Meesha Singh
- Department of Microbiology, St. Xavier's College, Kolkata 700016, India
| | - Sayak Ganguli
- Theoretical and Computational Biology Division, AIIST, Palta 742122, India
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20
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Aujoulat F, Pagès S, Masnou A, Emboulé L, Teyssier C, Marchandin H, Gaudriault S, Givaudan A, Jumas-Bilak E. The population structure of Ochrobactrum isolated from entomopathogenic nematodes indicates interactions with the symbiotic system. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 70:131-139. [PMID: 30790700 DOI: 10.1016/j.meegid.2019.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 10/14/2018] [Accepted: 02/16/2019] [Indexed: 02/02/2023]
Abstract
Entomopathogenic nematodes (EPNs) form specific mutualistic associations with bioluminescent enterobacteria. In Heterorhabditidis indica, Ochrobactrum spp. was identified beside the symbiont Photorhabdus luminescens but its involvement in the symbiotic association in the EPNs remains unclear. This study describe the population structure and the diversity in Ochrobactrum natural populations isolated from EPNs in the Caribbean basin in order to question the existence of EPN-specialized clones and to gain a better insight into Ochrobactrum-EPNs relationships. EPN-associated Ochrobactrum and Photorhabdus strains were characterized by multi-locus sequence typing, Pulsed-Field Gel Electrophoresis fingerprinting and phenotypic traits. Population study showed the absence of EPN-specialized clones in O. intermedium and O. anthropi but suggested the success of some particular lineages. A low level of genetic and genomic diversification of Ochrobactrum isolated from the natural population of Caribbean nematodes was observed comparatively to the diversity of human-associated Ochrobactrum strains. Correspondences between Ochrobactrum and P. luminescens PFGE clusters have been observed, particularly in the case of nematodes from Dominican Republic and Puerto Rico. O. intermedium and O. anthropi associated to EPNs formed less biofilm than human-associated strains. These results evoke interactions between Ochrobactrum and the EPN symbiotic system rather than transient contamination. The main hypothesis to investigate is a toxic/antitoxic relationship because of the ability of Ochrobactrum to resist to antimicrobial and toxic compounds produced by Photorhabdus.
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Affiliation(s)
- Fabien Aujoulat
- HydroSciences Montpellier, IRD, CNRS, Univ Montpellier, Montpellier, France
| | - Sylvie Pagès
- Diversité, Génomes & Interactions Microorganismes-Insectes, INRA, Univ Montpellier, Montpellier, France
| | - Agnès Masnou
- HydroSciences Montpellier, IRD, CNRS, Univ Montpellier, Montpellier, France
| | - Loic Emboulé
- CHU de Pointe-à-Pitre/Abymes, Pointe-à-Pitre, Guadeloupe, France
| | | | - Hélène Marchandin
- HydroSciences Montpellier, IRD, CNRS, Univ Montpellier, Montpellier, France
| | - Sophie Gaudriault
- Diversité, Génomes & Interactions Microorganismes-Insectes, INRA, Univ Montpellier, Montpellier, France
| | - Alain Givaudan
- Diversité, Génomes & Interactions Microorganismes-Insectes, INRA, Univ Montpellier, Montpellier, France
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, IRD, CNRS, Univ Montpellier, Montpellier, France.
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21
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Brink M, Rhode C, Macey BM, Christison KW, Roodt-Wilding R. Metagenomic assessment of body surface bacterial communities of the sea urchin, Tripneustes gratilla. Mar Genomics 2019; 47:100675. [PMID: 30962029 DOI: 10.1016/j.margen.2019.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/29/2019] [Accepted: 03/29/2019] [Indexed: 12/31/2022]
Abstract
Sea urchins, including Tripneustes gratilla, are susceptible to a disease known as bald sea urchin disease, which has the potential to lead to economic losses in this emerging aquaculture industry in South Africa. This disease is characterized by lesions that form on sea urchin exoskeletal surfaces. This study aimed to characterize the body surface bacterial communities associated with T. gratilla, using a 16S rDNA gene metagenomics approach, to provide insight into the bacterial agents associated with this aquaculture species, as well as with this balding disease. Bacterial samples were collected from non-lesioned healthy animals obtained from natural locations along the eastern coast of South Africa, as well as from different cultured cohorts: non-lesioned healthy-, lesioned diseased- and non-lesioned stressed animals. A total of 1,067,515 individual bacterial operational taxonomic units (OTUs) were identified, belonging to 133 family-, 123 genus- and 113 species level OTU groups. Alpha diversity analyses, based on Chao1, Shannon and Simpson indices, showed that there were no statistically significant differences (ANOVA; P > 0.05) between the respective cohorts, as all cohorts displayed a high degree of bacterial diversity. Similarly, beta diversity analyses (Non-metric multidimensional scaling) showed a large degree of overlapping OTUs across the four cohorts. Within each cohort, various OTUs commonly associated with marine environments were found, predominantly belonging to the families Vibrionaceae, Saprospiraceae, Flavobacteriaceae and Sphingomonadaceae. Differential abundance analysis (DESeq2) revealed that OTUs that are differentially abundant across cohorts were likely not responsible for this balding disease, suggesting that complex bacterial agents, rather than a specific pathogenic agent, are likely causing this disease. Furthermore, the putative metabolic functions assigned to the bacterial communities showed that heterotrophic bacteria appear to be responsible for tissue lysis of degrading animal matter. The results from this study, obtained through univariate and multivariate-based approaches, contributes to future management strategies of this emerging aquaculture species by providing insight into the bacterial communities associated with both natural and cultured environments.
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Affiliation(s)
- M Brink
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag X1, Stellenbosch, Western Cape 7602, South Africa
| | - C Rhode
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag X1, Stellenbosch, Western Cape 7602, South Africa
| | - B M Macey
- Department of Agriculture, Forestry and Fisheries, Aquaculture Research, Private Bag X2, Roggebaai, Western Cape 8012, South Africa
| | - K W Christison
- Department of Agriculture, Forestry and Fisheries, Aquaculture Research, Private Bag X2, Roggebaai, Western Cape 8012, South Africa; Biodiversity and Conservation Biology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - R Roodt-Wilding
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag X1, Stellenbosch, Western Cape 7602, South Africa.
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22
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Fraser MW, Gleeson DB, Grierson PF, Laverock B, Kendrick GA. Metagenomic Evidence of Microbial Community Responsiveness to Phosphorus and Salinity Gradients in Seagrass Sediments. Front Microbiol 2018; 9:1703. [PMID: 30105009 PMCID: PMC6077243 DOI: 10.3389/fmicb.2018.01703] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/09/2018] [Indexed: 12/17/2022] Open
Abstract
Sediment microorganisms can have profound influence on productivity and functioning of marine ecosystems through their critical roles in regulating biogeochemical processes. However, the identity of sediment microorganisms that mediate organic matter turnover and nutrient cycling in seagrass sediments is only poorly understood. Here, we used metagenomic sequencing to investigate shifts in the structure and functioning of the microbial community of seagrass sediments across a salinity and phosphorus (P) availability gradient in Shark Bay, WA, Australia. This iconic ecosystem is oligotrophic and hypersaline with abundant seagrass meadows that directly contribute Shark Bay's status as a World Heritage Site. We show that sediment phosphonate metabolism genes as well as enzyme activities increase in hypersaline conditions with lower soluble reactive phosphate in the water column. Given that sediment organic P content is also highest where P concentrations in the water column are low, we suggest that microbial processing of organic P can contribute to the P requirements of seagrasses at particularly oligotrophic sites. Seagrass meadows are often highly productive in oligotrophic waters, and our findings suggest that an increase in the functional capacity of microbial communities in seagrass sediments to break down organic P may contribute to the high productivity of seagrass meadows under oligotrophic conditions. When compared to soil and sediment metagenomes from other aquatic and terrestrial ecosystems, we also show microbial communities in seagrass sediments have a disproportionately high abundance of putative phosphorus and sulfur metabolism genes, which may have played an important evolutionary role in allowing these angiosperms to recolonize the marine environment and prosper under oligotrophic conditions.
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Affiliation(s)
- Matthew W. Fraser
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- Oceans Institute, The University of Western Australia, Crawley, WA, Australia
| | - Deirdre B. Gleeson
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Pauline F. Grierson
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Bonnie Laverock
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- Oceans Institute, The University of Western Australia, Crawley, WA, Australia
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Gary A. Kendrick
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- Oceans Institute, The University of Western Australia, Crawley, WA, Australia
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23
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Gonzalez-Escobedo R, Briones-Roblero CI, Pineda-Mendoza RM, Rivera-Orduña FN, Zúñiga G. Bacteriome from Pinus arizonica and P. durangensis: Diversity, Comparison of Assemblages, and Overlapping Degree with the Gut Bacterial Community of a Bark Beetle That Kills Pines. Front Microbiol 2018; 9:77. [PMID: 29441055 PMCID: PMC5797664 DOI: 10.3389/fmicb.2018.00077] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/12/2018] [Indexed: 02/01/2023] Open
Abstract
Symbioses between plants and microorganims have been fundamental in the evolution of both groups. The endophytic bacteria associated with conifers have been poorly studied in terms of diversity, ecology, and function. Coniferous trees of the genera Larix, Pseudotsugae, Picea and mainly Pinus, are hosts of many insects, including bark beetles and especially the Dendroctonus species. These insects colonize and kill these trees during their life cycle. Several bacteria detected in the gut and cuticle of these insects have been identified as endophytes in conifers. In this study, we characterized and compared the endophytic bacterial diversity in roots, phloem and bark of non-attacked saplings of Pinus arizonica and P. durangensis using 16S rRNA gene pyrosequencing. In addition, we evaluated the degree of taxonomic relatedness, and the association of metabolic function profiles of communities of endophytic bacteria and previously reported gut bacterial communities of D. rhizophagus; a specialized bark beetle that colonizes and kills saplings of these pine species. Our results showed that both pine species share a similar endophytic community. A total of seven bacterial phyla, 14 classes, 26 orders, 43 families, and 51 genera were identified. Enterobacteriaceae was the most abundant family across all samples, followed by Acetobacteraceae and Acidobacteriaceae, which agree with previous studies performed in other pines and conifers. Endophytic communities and that of the insect gut were significantly different, however, the taxonomic relatedness of certain bacterial genera of pines and insect assemblages suggested that some bacteria from pine tissues might be the same as those in the insect gut. Lastly, the metabolic profile using PICRUSt showed there to be a positive association between communities of both pines and insect gut. This study represents the baseline into the knowledge of the endophytic bacterial communities of two of the major hosts affected by D. rhizophagus.
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Affiliation(s)
- Roman Gonzalez-Escobedo
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Carlos I Briones-Roblero
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Rosa M Pineda-Mendoza
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Flor N Rivera-Orduña
- Laboratorio de Ecología Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Gerardo Zúñiga
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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24
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Sengupta S, Ganguli S, Singh PK. Metagenome analysis of the root endophytic microbial community of Indian rice ( O. sativa L.). GENOMICS DATA 2017; 12:41-43. [PMID: 28289604 PMCID: PMC5339402 DOI: 10.1016/j.gdata.2017.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 02/23/2017] [Indexed: 01/31/2023]
Abstract
This study reports the root endophytic microbial community profile in rice (Oryza sativa L.), the largest food crop of Asia, using 16S rRNA gene amplicon sequencing. Metagenome of OS01 and OS04 consisted of 11,17,900 sequences with 300 Mbp size and average 55.6% G + C content. Data of this study are available at NCBI Bioproject (PRJNA360379). The taxonomic analysis of 843 OTU's showed that the sequences belonged to four major phyla revealing dominance of Proteobacteria, Firmicutes, Cyanobacteria and Actinobacteria. Results reveal the dominance of Bacillus as major endophytic genera in rice roots, probably playing a key role in Nitrogen fixation.
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Affiliation(s)
- Subhadipa Sengupta
- Department of Botany, Bidhannagar College, EB-2, Sector-1, Salt Lake, Kolkata 700064, India
| | - Sayak Ganguli
- Theoretical and Computational Biology Division, AIIST, Palta 743122, India
| | - Pankaj K Singh
- Computational Biology Division, The Biome, Kolkata 700064, India
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25
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Torta L, Lo Piccolo S, Piazza G, Burruano S, Colombo P, Ottonello D, Perrone R, Di Maida G, Pirrotta M, Tomasello A, Calvo S. Lulwoana sp., a dark septate endophyte in roots of Posidonia oceanica (L.) Delile seagrass. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:505-511. [PMID: 25262834 DOI: 10.1111/plb.12246] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 08/03/2014] [Indexed: 06/03/2023]
Abstract
Posidonia oceanica is the most common, widespread and important monocotyledon seagrass in the Mediterranean Basin, and hosts a large biodiversity of species, including microorganisms with key roles in the marine environment. In this study, we ascertain the presence of a fungal endophyte in the roots of P. oceanica growing on different substrata (rock, sand and matte) in two Sicilian marine meadows. Staining techniques on root fragments and sections, in combination with microscope observations, were used to visualise the fungal presence and determine the percentage of fungal colonisation (FC) in this tissue. In root fragments, statistical analysis of the FC showed a higher mean in roots anchored on rock than on matte and sand. In root sections, an inter- and intracellular septate mycelium, producing intracellular microsclerotia, was detected from the rhizodermis to the vascular cylinder. Using isolation techniques, we obtained, from both sampling sites, sterile, slow-growing fungal colonies, dark in colour, with septate mycelium, belonging to the dark septate endophytes (DSEs). DNA sequencing of the internal transcribed spacer (ITS) region identified these colonies as Lulwoana sp. To our knowledge, this is the first report of Lulwoana sp. as DSE in roots of P. oceanica. Moreover, the highest fungal colonisation, detected in P. oceanica roots growing on rock, suggests that the presence of the DSE may help the host in several ways, particularly in capturing mineral nutrients through lytic activity.
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Affiliation(s)
- L Torta
- Dipartimento Scienze Agrarie e Forestali, Università di Palermo, Palermo, Italy
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Castro RA, Quecine MC, Lacava PT, Batista BD, Luvizotto DM, Marcon J, Ferreira A, Melo IS, Azevedo JL. Isolation and enzyme bioprospection of endophytic bacteria associated with plants of Brazilian mangrove ecosystem. SPRINGERPLUS 2014; 3:382. [PMID: 25110630 PMCID: PMC4125609 DOI: 10.1186/2193-1801-3-382] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/01/2014] [Indexed: 11/18/2022]
Abstract
The mangrove ecosystem is a coastal tropical biome located in the transition zone between land and sea that is characterized by periodic flooding, which confers unique and specific environmental conditions on this biome. In these ecosystems, the vegetation is dominated by a particular group of plant species that provide a unique environment harboring diverse groups of microorganisms, including the endophytic microorganisms that are the focus of this study. Because of their intimate association with plants, endophytic microorganisms could be explored for biotechnologically significant products, such as enzymes, proteins, antibiotics and others. Here, we isolated endophytic microorganisms from two mangrove species, Rhizophora mangle and Avicennia nitida, that are found in streams in two mangrove systems in Bertioga and Cananéia, Brazil. Bacillus was the most frequently isolated genus, comprising 42% of the species isolated from Cananéia and 28% of the species from Bertioga. However, other common endophytic genera such as Pantoea, Curtobacterium and Enterobacter were also found. After identifying the isolates, the bacterial communities were evaluated for enzyme production. Protease activity was observed in 75% of the isolates, while endoglucanase activity occurred in 62% of the isolates. Bacillus showed the highest activity rates for amylase and esterase and endoglucanase. To our knowledge, this is the first reported diversity analysis performed on endophytic bacteria obtained from the branches of mangrove trees and the first overview of the specific enzymes produced by different bacterial genera. This work contributes to our knowledge of the microorganisms and enzymes present in mangrove ecosystems.
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Affiliation(s)
- Renata A Castro
- />Center for Nuclear Energy in Agriculture (CENA), University of São Paulo, Piracicaba, SP Brazil
| | - Maria Carolina Quecine
- />Department of Genetics, Escola Superior de Agricultura, “Luiz de Queiroz” (ESALQ), University of São Paulo, Piracicaba, SP Brazil
| | - Paulo T Lacava
- />Department of Morphology and Pathology, Center for Biological and Health Sciences, Federal University of São Carlos (UFSCar), São Carlos, SP Brazil
| | - Bruna D Batista
- />Department of Genetics, Escola Superior de Agricultura, “Luiz de Queiroz” (ESALQ), University of São Paulo, Piracicaba, SP Brazil
| | - Danice M Luvizotto
- />Department of Genetics, Escola Superior de Agricultura, “Luiz de Queiroz” (ESALQ), University of São Paulo, Piracicaba, SP Brazil
| | - Joelma Marcon
- />Department of Genetics, Escola Superior de Agricultura, “Luiz de Queiroz” (ESALQ), University of São Paulo, Piracicaba, SP Brazil
| | - Anderson Ferreira
- />Brazilian Agricultural Research Corporation – Embrapa Agrosilvopastoral, Sinop, MS Brazil
| | - Itamar S Melo
- />Laboratory of Environmental Microbiology, CNPMA — Embrapa Environment, Jaguariúna, SP Brazil
| | - João L Azevedo
- />Center for Nuclear Energy in Agriculture (CENA), University of São Paulo, Piracicaba, SP Brazil
- />Department of Genetics, Escola Superior de Agricultura, “Luiz de Queiroz” (ESALQ), University of São Paulo, Piracicaba, SP Brazil
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Luna GM, Corinaldesi C, Rastelli E, Danovaro R. Patterns and drivers of bacterial α- and β-diversity across vertical profiles from surface to subsurface sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:731-739. [PMID: 24115624 DOI: 10.1111/1758-2229.12075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/08/2013] [Indexed: 06/02/2023]
Abstract
We investigated the patterns and drivers of bacterial α- and β-diversity, along with viral and prokaryotic abundance and the carbon production rates, in marine surface and subsurface sediments (down to 1 m depth) in two habitats: vegetated sediments (seagrass meadow) and non-vegetated sediments. Prokaryotic abundance and production decreased with depth in the sediment, but cell-specific production rates and the virus-to-prokaryote ratio increased, highlighting unexpectedly high activity in the subsurface. The highest diversity was observed in vegetated sediments. Bacterial β-diversity between sediment horizons was high, and only a minor number of taxa was shared between surface and subsurface layers. Viruses significantly contributed to explain α- and β-diversity patterns. Despite potential limitations due to the only use of fingerprinting techniques, this study indicates that the coastal subsurface host highly active and diversified bacterial assemblages, that subsurface cells are more active than expected and that viruses promote β-diversity and stimulate bacterial metabolism in subsurface layers. The limited number of taxa shared between habitats, and between surface and subsurface sediment horizons, suggests that future investigations of the shallow subsurface will provide insights into the census of bacterial diversity, and the comprehension of the patterns and drivers of prokaryotic diversity in marine ecosystems.
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Affiliation(s)
- Gian Marco Luna
- Institute of Marine Sciences (CNR - ISMAR), National Research Council, Castello 2737/f, Arsenale - Tesa 104, 30122, Venezia, Italy
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Plant growth promotion potential is equally represented in diverse grapevine root-associated bacterial communities from different biopedoclimatic environments. BIOMED RESEARCH INTERNATIONAL 2013; 2013:491091. [PMID: 23878810 PMCID: PMC3708380 DOI: 10.1155/2013/491091] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/14/2013] [Accepted: 05/21/2013] [Indexed: 11/18/2022]
Abstract
Plant-associated bacteria provide important services to host plants. Environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. However, whether these environmental factors may influence the plant growth promoting (PGP) potential of the root-associated bacteria is not widely understood. To address this issue, the diversity and PGP potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three Mediterranean environments along a macrotransect identifying an aridity gradient were assessed by culture-dependent and independent approaches. According to 16S rRNA gene PCR-DGGE, the structure of endosphere and rhizosphere bacterial communities was highly diverse (P = 0.03) and was associated with a cultivar/latitudinal/climatic effect. Despite being diverse, the bacterial communities associated with Egyptian grapevines shared a higher similarity with the Tunisian grapevines than those cultivated in North Italy. A similar distribution, according to the cultivar/latitude/aridity gradients, was observed for the cultivable bacteria. Many isolates (23%) presented in vitro multiple stress resistance capabilities and PGP activities, the most frequent being auxin synthesis (82%), insoluble phosphate solubilisation (61%), and ammonia production (70%). The comparable numbers and types of potential PGP traits among the three different environmental settings indicate a strong functional homeostasis of beneficial bacteria associated with grape root.
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Grossart HP, Riemann L, Tang KW. Molecular and functional ecology of aquatic microbial symbionts. Front Microbiol 2013; 4:59. [PMID: 23509443 PMCID: PMC3597942 DOI: 10.3389/fmicb.2013.00059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 02/28/2013] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hans-Peter Grossart
- Department of Experimental Limnology, IGB-Leibniz-Institute of Freshwater Ecology and Inland Fisheries Berlin, Germany ; Institute of Biochemistry and Biology, Potsdam University Potsdam, Germany
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