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Melchior PP, Reiss E, Payne Z, Vuong N, Hovorka K, Lindsay HL, Diaz GR, Gaire T, Noyes N. Analysis of the northern pitcher plant (Sarracenia purpurea L.) phytotelm bacteriome throughout a temperate region growing season. PLoS One 2024; 19:e0306602. [PMID: 38995889 PMCID: PMC11244801 DOI: 10.1371/journal.pone.0306602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
The insectivorous Northern Pitcher Plant, Sarracenia purpurea, recruits a dynamic biotic community in the rainwater collected by its pitcher-shaped leaves. Insect capture and degradation within the pitcher fluid (phytotelma) has been well documented as a mechanism for supplementing the plant's nitrogen, phosphorous, and micronutrient requirements. Metagenomic studies have shown a diverse microbiome in this phytotelm environment, including taxa that contribute metabolically to prey digestion. In this investigation, we used high-throughput 16S rDNA sequencing and bioinformatics to analyze the S. purpurea phytotelm bacteriome as it changes through the growing season (May-September) in plants from the north-central region of the species' native range. Additionally, we used molecular techniques to detect and quantify bacterial nitrogenase genes (nifH) in all phytotelm samples to explore the hypothesis that diazotrophy is an additional mechanism of supplying biologically available nitrogen to S. purpurea. The results of this study indicate that while prokaryote diversity remains relatively stable in plants at different locations within our region, diversity changes significantly as the growing season progresses. Furthermore, nifH genes were detected at biologically significant concentrations in one hundred percent of samples, suggesting that nitrogen fixation may be an important contributor to the S. purpurea nutrient budget.
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Affiliation(s)
- Paul P. Melchior
- Department of Biology, North Hennepin Community College, Brooklyn Park, Minnesota, United States of America
- Department of Biology, Bemidji State University, Bemidji, Minnesota, United States of America
- Department of Marine Science, Atlantic Technological University, Galway, Republic of Ireland
- Department of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Emma Reiss
- Department of Biology, North Hennepin Community College, Brooklyn Park, Minnesota, United States of America
- Department of Biology, Bemidji State University, Bemidji, Minnesota, United States of America
| | - Zachary Payne
- Department of Biology, North Hennepin Community College, Brooklyn Park, Minnesota, United States of America
- Department of Biology, Bemidji State University, Bemidji, Minnesota, United States of America
| | - Nhi Vuong
- Department of Biology, North Hennepin Community College, Brooklyn Park, Minnesota, United States of America
- Department of Biology, Bemidji State University, Bemidji, Minnesota, United States of America
| | - Kari Hovorka
- Department of Biology, North Hennepin Community College, Brooklyn Park, Minnesota, United States of America
- Department of Biology, Bemidji State University, Bemidji, Minnesota, United States of America
| | - Hunter L. Lindsay
- Department of Biology, North Hennepin Community College, Brooklyn Park, Minnesota, United States of America
- Department of Biology, Bemidji State University, Bemidji, Minnesota, United States of America
| | - Gerardo R. Diaz
- Department of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Tara Gaire
- Department of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Noelle Noyes
- Department of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
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Grothjan JJ, Young EB. Bacterial Recruitment to Carnivorous Pitcher Plant Communities: Identifying Sources Influencing Plant Microbiome Composition and Function. Front Microbiol 2022; 13:791079. [PMID: 35359741 PMCID: PMC8964293 DOI: 10.3389/fmicb.2022.791079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Processes influencing recruitment of diverse bacteria to plant microbiomes remain poorly understood. In the carnivorous pitcher plant Sarracenia purpurea model system, individual pitchers open to collect rainwater, invertebrates and a diverse microbial community, and this detrital food web is sustained by captured insect prey. This study examined how potential sources of bacteria affect the development of the bacterial community within pitchers, how the host plant tissue affects community development and how established vs. assembling communities differ. In a controlled greenhouse experiment, seven replicate pitchers were allocated to five treatments to exclude specific bacterial sources or host tissue: milliQ water only, milliQ + insect prey, rainwater + prey, established communities + prey, artificial pitchers with milliQ + prey. Community composition and functions were examined over 8-40 weeks using bacterial gene sequencing and functional predictions, measurements of cell abundance, hydrolytic enzyme activity and nutrient transformations. Distinct community composition and functional differences between artificial and real pitchers confirm an important influence of host plant tissue on community development, but also suggest this could be partially related to host nutrient uptake. Significant recruitment of bacteria to pitchers from air was evident from many taxa common to all treatments, overlap in composition between milliQ, milliQ + prey, and rainwater + prey treatments, and few taxa unique to milliQ only pitchers. Community functions measured as hydrolytic enzyme (chitinase, protease) activity suggested a strong influence of insect prey additions and were linked to rapid transformation of insect nutrients into dissolved and inorganic sources. Bacterial taxa found in 6 of 7 replicate pitchers within treatments, the "core microbiome" showed tighter successional trajectories over 8 weeks than all taxa. Established pitcher community composition was more stable over 8 weeks, suggesting a diversity-stability relationship and effect of microinvertebrates on bacteria. This study broadly demonstrates that bacterial composition in host pitcher plants is related to both stochastic and specific bacterial recruitment and host plants influence microbial selection and support microbiomes through capture of insect prey.
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Affiliation(s)
- Jacob J. Grothjan
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Erica B. Young
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
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Selective Bacterial Community Enrichment between the Pitcher Plants Sarracenia minor and Sarracenia flava. Microbiol Spectr 2021; 9:e0069621. [PMID: 34817222 PMCID: PMC8612160 DOI: 10.1128/spectrum.00696-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The interconnected and overlapping habitats present in natural ecosystems remain a challenge in determining the forces driving microbial community composition. The cuplike leaf structures of some carnivorous plants, including those of the family Sarraceniaceae, are self-contained ecological habitats that represent systems for exploring such microbial ecology questions. We investigated whether Sarracenia minor and Sarracenia flava cultivate distinct bacterial communities when sampled at the same geographic location and time. This sampling strategy eliminates many abiotic environmental variables present in other studies that compare samples harvested over time, and it could reveal biotic factors driving the selection of microbes. DNA extracted from the decomposing detritus trapped in each Sarracenia leaf pitcher was profiled using 16S rRNA amplicon sequencing. We identified a surprising amount of bacterial diversity within each pitcher, but we also discovered bacteria whose abundance was specifically enriched in one of the two Sarracenia species. These differences in bacterial community representation suggest some biotic influence of the Sarracenia plant on the bacterial composition of their pitchers. Overall, our results suggest that bacterial selection due to factors other than geographic location, weather, or prey availability is occurring within the pitchers of these two closely related plant species. This indicates that specific characteristics of S. minor and S. flava may play a role in fostering distinct bacterial communities. These confined, naturally occurring microbial ecosystems within Sarracenia pitchers may provide model systems to answer important questions about the drivers of microbial community composition, succession, and response to environmental perturbations. IMPORTANCE This study uses amplicon sequencing to compare the bacterial communities of environmental samples from the detritus of the leaf cavities of Sarracenia minor and Sarracenia flava pitcher plants. We sampled the detritus at the same time and in the same geographic location, eliminating many environmental variables present in other comparative studies. This study revealed that different species of Sarracenia contain distinct bacterial members within their pitchers, suggesting that these communities are not randomly established based on environmental factors and the prey pool but are potentially enriched for by the plants' chemical or physical environment. This study of these naturally occurring, confined microbial ecosystems will help further establish carnivorous pitcher plants as a model system for answering important questions about the development and succession of microbial communities.
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Sickel W, Van de Weyer AL, Bemm F, Schultz J, Keller A. Venus flytrap microbiotas withstand harsh conditions during prey digestion. FEMS Microbiol Ecol 2019; 95:5289860. [PMID: 30649283 DOI: 10.1093/femsec/fiz010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
The carnivorous Venus flytrap (Dionaea muscipula) overcomes environmental nutrient limitation by capturing small animals. Such prey is digested with an acidic enzyme-containing mucilage that is secreted into the closed trap. However, surprisingly little is known about associations with microorganisms. Therefore, we assessed microbiotas of traps and petioles for the Venus flytrap by 16S amplicon meta-barcoding. We also performed time-series assessments of dynamics during digestion in traps and experimental acidification of petioles. We found that the traps hosted distinct microbiotas that differed from adjacent petioles. Further, they showed a significant taxonomic turnover during digestion. Following successful catches, prey-associated bacteria had strong effects on overall composition. With proceeding digestion, however, microbiotas were restored to compositions resembling pre-digestion stages. A comparable, yet less extensive shift was found when stimulating digestion with coronatine. Artificial acidification of petioles did not induce changes towards trap-like communities. Our results show that trap microbiota were maintained during digestion despite harsh conditions and recovered after short-term disturbances through prey microbiota. This indicates trap-specific and resilient associations. By mapping to known genomes, we predicted putative adaptations and functional implications for the system, yet direct mechanisms and quantification of host benefits, like the involvement in digestion, remain to be addressed.
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Affiliation(s)
- Wiebke Sickel
- Molecular Biodiversity Group, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Felix Bemm
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jörg Schultz
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Center for Computational and Theoretical Biology, University of Würzburg, Germany
| | - Alexander Keller
- Molecular Biodiversity Group, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Center for Computational and Theoretical Biology, University of Würzburg, Germany
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Grothjan JJ, Young EB. Diverse microbial communities hosted by the model carnivorous pitcher plant Sarracenia purpurea: analysis of both bacterial and eukaryotic composition across distinct host plant populations. PeerJ 2019; 7:e6392. [PMID: 30805246 PMCID: PMC6383556 DOI: 10.7717/peerj.6392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/04/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The pitcher plant Sarracenia purpurea supplements nutrient acquisition through carnivory, capturing insect prey which are digested by a food web community of eukaryotes and bacteria. While the food web invertebrates are well studied, and some recent studies have characterized bacteria, detailed genetic analysis of eukaryotic diversity is lacking. This study aimed to compare eukaryotic and bacterial composition and diversity of pitcher communities within and between populations of host plants in nearby but distinct wetland habitats, and to characterize microbial functions across populations and in comparison with another freshwater community. METHODS Pitcher fluid was sampled from the two wetlands, Cedarburg and Sapa Bogs, community DNA was extracted, and 16S and 18S rRNA amplicons were sequenced and data processed for community-level comparisons. RESULTS AND CONCLUSIONS Bacterial diversity in the small pitcher volume rivaled that of larger aquatic communities. Between pitcher plant populations, several bacterial families (Kiloniellaceae, Acetobacteraceae, Xanthobacteraceae, Sanguibacteraceae, Oligoflexaceae, Nitrosomonadaceae, Chromatiaceae, Saprospiraceae) were significantly higher in one population. However, although predicted pitcher bacterial functions were distinct from other freshwater communities, especially for some amino acid metabolism, functions were similar across all the pitchers in the two populations. This suggests some functional redundancy among bacterial taxa, and that functions converge to achieve similar food web processes. The sequencing identified a previously under-appreciated high diversity of ciliates, Acari mites, fungi and flagellates in pitcher communities; the most abundant sequences from eukaryotic taxa were Oligohymenophorea ciliates, millipedes and Ichthyosporea flagellates. Two thirds of taxa were identified as food web inhabitants and less than one third as prey organisms. Although eukaryotic composition was not significantly different between populations, there were different species of core taxonomic groups present in different pitchers-these differences may be driven by wetland habitats providing different populations to colonize new pitchers. Eukaryotic composition was more variable than bacterial composition, and there was a poor relationship between bacterial and eukaryotic composition within individual pitchers, suggesting that colonization by eukaryotes may be more stochastic than for bacteria, and bacterial recruitment to pitchers may involve factors other than prey capture and colonization by eukaryotic food web inhabitants.
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Affiliation(s)
- Jacob J. Grothjan
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States of America
| | - Erica B. Young
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States of America
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States of America
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Integrated Hydrolysis of Mixed Agro-Waste for a Second Generation Biorefinery Using Nepenthes mirabilis Pod Digestive Fluids. Processes (Basel) 2019. [DOI: 10.3390/pr7020064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
To sustainably operate a biorefinery with a low cost input in a commercial setting, the hydrolysis of lignocellulosic biomass must be undertaken in a manner which will impart environmental tolerance while reducing fermenter inhibitors from the delignification process. The challenge lies with the highly recalcitrant lignin structure, which limits the conversion of the holocelluloses to fermentable total reducing sugars (TRS). Due to these challenges, sustainable and innovative methods to pre-treat biomass must be developed for delignocellulolytic operations. Herein, Nepenthes mirabilis digestive fluids shown to have ligninolytic, cellulolytic and xylanolytic activities were used as an enzyme cocktail to hydrolyse mixed agro-waste constituted by Citrus sinensis (orange), Malus domestica (apple) peels, cobs from Zea mays (maize) and Quercus robur (oak) yard waste. The digestive fluids contained carboxylesterases (529.41 ± 30.50 U/L), β-glucosidases (251.94 ± 11.48 U/L) and xylanases (36.09 ± 18.04 U/L), constituting an enzymatic cocktail with significant potential for the reduction in total residual phenolic compounds (TRPCs), while being appropriate for holocellulose hydrolysis. Furthermore, the maximum TRS obtainable was 310 ± 5.19 mg/L within 168 h, while the TRPCs were reduced from 6.25 ± 0.18 to 4.26 ± 0.09 mg/L, which was lower than that observed when conventional methods were used. Overall, N. mirabilis digestive fluids demonstrated an ability to support biocatalytic processes with minimised cellulases hydrolysis interference. Therefore, the digestive enzymes in N. mirabilis pods can be used in an integrated system for feedstock hydrolysis in a second generation biorefinery.
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Young EB, Sielicki J, Grothjan JJ. Regulation of Hydrolytic Enzyme Activity in Aquatic Microbial Communities Hosted by Carnivorous Pitcher Plants. MICROBIAL ECOLOGY 2018; 76:885-898. [PMID: 29679120 DOI: 10.1007/s00248-018-1187-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
Carnivorous pitcher plants Sarracenia purpurea host diverse eukaryotic and bacterial communities which aid in insect prey digestion, but little is known about the functional processes mediated by the microbial communities. This study aimed to connect pitcher community diversity with functional nutrient transformation processes, identifying bacterial taxa, and measuring regulation of hydrolytic enzyme activity in response to prey and alternative nutrient sources. Genetic analysis identified diverse bacterial taxa known to produce hydrolytic enzyme activities. Chitinase, protease, and phosphatase activities were measured using fluorometric assays. Enzyme activity in field pitchers was positively correlated with bacterial abundance, and activity was suppressed by antibiotics suggesting predominantly bacterial sources of chitinase and protease activity. Fungi, algae, and rotifers observed could also contribute enzyme activity, but fresh insect prey released minimal chitinase activity. Activity of chitinase and proteases was upregulated in response to insect additions, and phosphatase activity was suppressed by phosphate additions. Particulate organic P in prey was broken down, appearing as increasing dissolved organic and inorganic P pools within 14 days. Chitinase and protease were not significantly suppressed by availability of dissolved organic substrates, though organic C and N stimulated bacterial growth, resulting in elevated enzyme activity. This comprehensive field and experimental study show that pitcher plant microbial communities dynamically regulate hydrolytic enzyme activity, to digest prey nutrients to simpler forms, mediating biogeochemical nutrient transformations and release of nutrients for microbial and host plant uptake.
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Affiliation(s)
- Erica B Young
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N Maryland Ave, Milwaukee, WI, 53211, USA.
| | - Jessica Sielicki
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N Maryland Ave, Milwaukee, WI, 53211, USA
| | - Jacob J Grothjan
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N Maryland Ave, Milwaukee, WI, 53211, USA
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Kokubun T. Occurrence of myo-inositol and alkyl-substituted polysaccharide in the prey-trapping mucilage of Drosera capensis. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2017; 104:83. [PMID: 28940006 PMCID: PMC5610204 DOI: 10.1007/s00114-017-1502-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/29/2017] [Accepted: 09/01/2017] [Indexed: 11/25/2022]
Abstract
The chemical composition of the exudate mucilage droplets of the carnivorous plant Drosera capensis was investigated using nuclear magnetic resonance spectroscopy. The mucilage was found to contain beside a very large molecular weight polysaccharide a significant amount of myo-inositol. It appears that myo-inositol escaped detection due to the commonly applied methodology on the chemical analysis of plant mucilage, such as dialysis, precipitation of polysaccharide component with alcohol, acid hydrolysis and detection of the resultant monosaccharide (aldose) units. The possible functions of myo-inositol in the mucilage droplets and the fate after being washed off from the leaf tentacles are proposed. On the polysaccharide component, the presence of methyl ester and alkyl chain-like moieties could be confirmed. These lipophilic moieties may provide the prey-trapping mucilage with the unique adhesive property onto the hydrophobic insect body parts, as well as onto the nature's well-known superhydrophobic surfaces such as the leaves of the sacred lotus plants. A re-evaluation of the mineral components of the mucilage, reported 40 years ago, is presented from the viewpoints of the current result and plants' natural habitat. A case for re-examination of the well-studied plant mucilaginous materials is made in light of the new findings.
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Affiliation(s)
- Tetsuo Kokubun
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.
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Kanokratana P, Mhuanthong W, Laothanachareon T, Tangphatsornruang S, Eurwilaichitr L, Kruetreepradit T, Mayes S, Champreda V. Comparative Study of Bacterial Communities in Nepenthes Pitchers and Their Correlation to Species and Fluid Acidity. MICROBIAL ECOLOGY 2016; 72:381-93. [PMID: 27287538 DOI: 10.1007/s00248-016-0798-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 05/31/2016] [Indexed: 05/24/2023]
Abstract
Pitchers are specialized digestive organs of carnivorous plants which evolved for trapping prey and represent a unique environment harboring hidden diversity of unexplored microbes forming transient hydrolytic microcosms. In this study, the diversity of bacterial communities in the pitcher fluids of seven local Nepenthes found in Thailand was assessed by tagged 16S ribosomal RNA (rRNA) gene amplicon sequencing on an Ion PGM™ platform. A total of 1,101,000 filtered sequences were obtained which were taxonomically classified into 20 phyla, 48 classes, 72 orders, 153 families, and 442 genera while the remainder (1.43 %) could not be assigned to any existing taxa. Proteobacteria represented the predominant members in closed pitchers and more diversified bacterial taxa particularly Bacteriodetes and Actinobacteria, showed increasing abundance in open pitchers containing insect bodies. Principal coordinate analysis revealed that distribution of bacterial taxa was not significantly related to the Nepenthes species but strongly correlated to the pH of the pitcher fluids (pH 1.7-6.7). Acidicella was a highly dominant bacterial genus in acidic pitcher fluids while Dyella and Mycobacterium were also common genera in most pitchers. A unique microbial community structure was found in Nepenthes ampullaria which could reflect their adaptation to digest leaf litter, in addition to insect prey. The work revealed the highly unexplored nature of bacterial microcosms in Nepenthes pitcher fluids and provides insights into their community structure in this unique ecological system.
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Affiliation(s)
- Pattanop Kanokratana
- Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Paholyothin Road, Khlong Luang, Pathumthani, 12120, Thailand.
| | - Wuttichai Mhuanthong
- Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Paholyothin Road, Khlong Luang, Pathumthani, 12120, Thailand
| | - Thanaporn Laothanachareon
- Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Paholyothin Road, Khlong Luang, Pathumthani, 12120, Thailand
| | - Sithichoke Tangphatsornruang
- Genome Institute, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathumthani, 12120, Thailand
| | - Lily Eurwilaichitr
- Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Paholyothin Road, Khlong Luang, Pathumthani, 12120, Thailand
| | - Trongtham Kruetreepradit
- Southeast Asian Nepenthes Study and Research Foundation (SEANSRF), PO Box 36, Lamai, Koh Samui, Suratthani, 84310, Thailand
| | - Shawn Mayes
- Southeast Asian Nepenthes Study and Research Foundation (SEANSRF), PO Box 36, Lamai, Koh Samui, Suratthani, 84310, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Paholyothin Road, Khlong Luang, Pathumthani, 12120, Thailand
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Sickel W, Grafe TU, Meuche I, Steffan-Dewenter I, Keller A. Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies. MICROBIAL ECOLOGY 2016; 71:938-53. [PMID: 26790863 DOI: 10.1007/s00248-015-0723-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 12/21/2015] [Indexed: 05/25/2023]
Abstract
Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their pitcher-mediated nutrient sources, sequestering nitrogen from arthropod prey and arthropods as well as bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial richness and community structure were similar in leaves, peristomes, inside and outside walls of both plant species. Regarding digestive fluids, bacterial richness was higher in N. hemsleyana than in N. rafflesiana. Additionally, digestive fluid communities were highly variable in structure, with strain-specific differences in community composition between replicates. Acidophilic taxa were mostly of low abundance, except the genus Acidocella, which strikingly reached extremely high levels in two N. rafflesiana fluids. In N. hemsleyana fluid, some taxa classified as vertebrate gut symbionts as well as saprophytes were enriched compared to N. rafflesiana, with saprophytes constituting potential competitors for nutrients. The high variation in community structure might be caused by a number of biotic and abiotic factors. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and/or rare encounters with bats.
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Affiliation(s)
- Wiebke Sickel
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - T Ulmar Grafe
- Faculty of Science, University Brunei Darussalam, Tungku Link, Gadong, BE, 1410, Brunei
| | - Ivonne Meuche
- Faculty of Science, University Brunei Darussalam, Tungku Link, Gadong, BE, 1410, Brunei
| | - Ingolf Steffan-Dewenter
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
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Cao HX, Schmutzer T, Scholz U, Pecinka A, Schubert I, Vu GTH. Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species. Front Microbiol 2015; 6:526. [PMID: 26236284 PMCID: PMC4500957 DOI: 10.3389/fmicb.2015.00526] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/12/2015] [Indexed: 01/21/2023] Open
Abstract
In the carnivorous plant genus Genlisea a unique lobster pot trapping mechanism supplements nutrition in nutrient-poor habitats. A wide spectrum of microbes frequently occurs in Genlisea's leaf-derived traps without clear relevance for Genlisea carnivory. We sequenced the metatranscriptomes of subterrestrial traps vs. the aerial chlorophyll-containing leaves of G. nigrocaulis and of G. hispidula. Ribosomal RNA assignment revealed soil-borne microbial diversity in Genlisea traps, with 92 genera of 19 phyla present in more than one sample. Microbes from 16 of these phyla including proteobacteria, green algae, amoebozoa, fungi, ciliates and metazoans, contributed additionally short-lived mRNA to the metatranscriptome. Furthermore, transcripts of 438 members of hydrolases (e.g., proteases, phosphatases, lipases), mainly resembling those of metazoans, ciliates and green algae, were found. Compared to aerial leaves, Genlisea traps displayed a transcriptional up-regulation of endogenous NADH oxidases generating reactive oxygen species as well as of acid phosphatases for prey digestion. A leaf-vs.-trap transcriptome comparison reflects that carnivory provides inorganic P- and different forms of N-compounds (ammonium, nitrate, amino acid, oligopeptides) and implies the need to protect trap cells against oxidative stress. The analysis elucidates a complex food web inside the Genlisea traps, and suggests ecological relationships between this plant genus and its entrapped microbiome.
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Affiliation(s)
- Hieu X. Cao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Thomas Schmutzer
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Uwe Scholz
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ)Köln, Germany
| | - Ingo Schubert
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
- Faculty of Science and Central European Institute of Technology, Masaryk UniversityBrno, Czech Republic
| | - Giang T. H. Vu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
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Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes. Syst Appl Microbiol 2015; 38:330-9. [DOI: 10.1016/j.syapm.2015.05.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 05/18/2015] [Accepted: 05/26/2015] [Indexed: 01/06/2023]
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Paisie TK, Miller TE, Mason OU. Effects of a ciliate protozoa predator on microbial communities in pitcher plant (Sarracenia purpurea) leaves. PLoS One 2014; 9:e113384. [PMID: 25423622 PMCID: PMC4244144 DOI: 10.1371/journal.pone.0113384] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/24/2014] [Indexed: 11/18/2022] Open
Abstract
The aquatic communities found within the water filled leaves of the pitcher plant, Sarracenia purpurea, have a simple trophic structure providing an ideal system to study microscale interactions between protozoan predators and their bacterial prey. In this study, replicate communities were maintained with and without the presence of the bactivorous protozoan, Colpoda steinii, to determine the effects of grazing on microbial communities. Changes in microbial (Archaea and Bacteria) community structure were assessed using iTag sequencing of 16S rRNA genes. The microbial communities were similar with and without the protozoan predator, with>1000 species. Of these species, Archaea were negligible, with Bacteria comprising 99.99% of the microbial community. The Proteobacteria and Bacteroidetes were the most dominant phyla. The addition of a protozoan predator did not have a significant effect on microbial evenness nor richness. However, the presence of the protozoan did cause a significant shift in the relative abundances of a number of bacterial species. This suggested that bactivorous protozoan may target specific bacterial species and/or that certain bacterial species have innate mechanisms by which they evade predators. These findings help to elucidate the effect that trophic structure perturbations have on predator prey interactions in microbial systems.
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Affiliation(s)
- Taylor K Paisie
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, United States of America
| | - Thomas E Miller
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Olivia U Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, United States of America
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14
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Chou LY, Clarke CM, Dykes GA. Bacterial communities associated with the pitcher fluids of three Nepenthes (Nepenthaceae) pitcher plant species growing in the wild. Arch Microbiol 2014; 196:709-17. [PMID: 25005571 DOI: 10.1007/s00203-014-1011-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/06/2014] [Accepted: 06/28/2014] [Indexed: 02/05/2023]
Abstract
Nepenthes pitcher plants produce modified jug-shaped leaves to attract, trap and digest insect prey. We used 16S rDNA cloning and sequencing to compare bacterial communities in pitcher fluids of each of three species, namely Nepenthes ampullaria, Nepenthes gracilis and Nepenthes mirabilis, growing in the wild. In contrast to previous greenhouse-based studies, we found that both opened and unopened pitchers harbored bacterial DNA. Pitchers of N. mirabilis had higher bacterial diversity as compared to other Nepenthes species. The composition of the bacterial communities could be different between pitcher types for N. mirabilis (ANOSIM: R = 0.340, p < 0.05). Other Nepenthes species had similar bacterial composition between pitcher types. SIMPER showed that more than 50 % of the bacterial taxa identified from the open pitchers of N. mirabilis were not found in other groups. Our study suggests that bacteria in N. mirabilis are divided into native and nonnative groups.
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Affiliation(s)
- Lee Yiung Chou
- School of Science, Monash University, Jalan Lagoon Selatan, 46150, Bandar Sunway, Selangor, Malaysia
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15
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Abstract
Fungal endophytes were isolated from 4 species of the carnivorous pitcher plant genus Sarracenia: S. minor, S. oreophila, S. purpurea, and S. psittacina. Twelve taxa of fungi, 8 within the Ascomycota and 4 within the Basidiomycota, were identified based on PCR amplification and sequencing of the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS rDNA) with taxonomic identity assigned using the NCBI nucleotide megablast search tool. Endophytes are known to produce a large number of metabolites, some of which may contribute to the protection and survival of the host. We speculate that endophyte-infected Sarracenia may benefit from their fungal associates by their influence on nutrient availability from within pitchers and, possibly, by directly influencing the biota within pitchers.
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Affiliation(s)
- Anthony Glenn
- Toxicology and Mycotoxin Research Unit, Russell Research Center, United State Department of Agriculture Agricultural Research Service, Athens, Georgia, United States of America
| | - Michael S. Bodri
- Department of Biology, North Georgia College & State University, Dahlonega, Georgia, United States of America
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16
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Alvarez-Pérez S, Herrera CM, de Vega C. Zooming-in on floral nectar: a first exploration of nectar-associated bacteria in wild plant communities. FEMS Microbiol Ecol 2012; 80:591-602. [PMID: 22324904 DOI: 10.1111/j.1574-6941.2012.01329.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Revised: 01/31/2012] [Accepted: 01/31/2012] [Indexed: 11/29/2022] Open
Abstract
Floral nectar of some animal-pollinated plants usually harbours highly adapted yeast communities which can profoundly alter nectar characteristics and, therefore, potentially have significant impacts on plant reproduction through their effects on insect foraging behaviour. Bacteria have also been occasionally observed in floral nectar, but their prevalence, phylogenetic diversity and ecological role within plant-pollinator-yeast systems remains unclear. Here we present the first reported survey of bacteria in floral nectar from a natural plant community. Culturable bacteria occurring in a total of 71 nectar samples collected from 27 South African plant species were isolated and identified by 16S rRNA gene sequencing. Rarefaction-based analyses were used to assess operational taxonomic units (OTUs) richness at the plant community level using nectar drops as sampling units. Our results showed that bacteria are common inhabitants of floral nectar of South African plants (53.5% of samples yielded growth), and their communities are characterized by low species richness (18 OTUs at a 16S rRNA gene sequence dissimilarity cut-off of 3%) and moderate phylogenetic diversity, with most isolates belonging to the Gammaproteobacteria. Furthermore, isolates showed osmotolerance, catalase activity and the ability to grow under microaerobiosis, three traits that might help bacteria to overcome important factors limiting their survival and/or growth in nectar.
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Affiliation(s)
- Sergio Alvarez-Pérez
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Sevilla, Spain.
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17
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Krieger JR, Kourtev PS. Bacterial diversity in three distinct sub-habitats within the pitchers of the northern pitcher plant, Sarracenia purpurea. FEMS Microbiol Ecol 2011; 79:555-67. [DOI: 10.1111/j.1574-6941.2011.01240.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 09/14/2011] [Accepted: 10/24/2011] [Indexed: 01/20/2023] Open
Affiliation(s)
- Joseph R. Krieger
- Department of Biology; Central Michigan University; Mt. Pleasant; MI; USA
| | - Peter S. Kourtev
- Department of Biology; Central Michigan University; Mt. Pleasant; MI; USA
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18
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Morohoshi T, Oikawa M, Sato S, Kikuchi N, Kato N, Ikeda T. Isolation and characterization of novel lipases from a metagenomic library of the microbial community in the pitcher fluid of the carnivorous plant Nepenthes hybrida. J Biosci Bioeng 2011; 112:315-20. [PMID: 21778111 DOI: 10.1016/j.jbiosc.2011.06.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 06/20/2011] [Accepted: 06/22/2011] [Indexed: 10/18/2022]
Abstract
Members of the genus Nepenthes are carnivorous plants that use the pitfall method of insect capture as a supplementary nutritional source. We extracted metagenomic DNA from the microbial community found in the pitcher fluid of Nepenthes and constructed a plasmid-based metagenomic library. An activity-based screening method enabled the isolation of two lipase genes, lip1 and lip2. Both Lip1 and Lip2 belong to a novel family or subfamily of lipases and show lipase activities in acidic conditions, such as those found in pitcher fluid. This study was conducted under the assumption that the secreted Lip1 and Lip2 were capable of enzymatic activity in the acidic pitcher fluid.
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Affiliation(s)
- Tomohiro Morohoshi
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University, 7-1-2 Yoto, Utsunomiya 321-8585, Japan.
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19
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Sirov D, Borovec J, Picek TX, Adamec LR, Nedbalov L, Vrba J. Ecological implications of organic carbon dynamics in the traps of aquatic carnivorous Utricularia plants. FUNCTIONAL PLANT BIOLOGY : FPB 2011; 38:583-593. [PMID: 32480911 DOI: 10.1071/fp11023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Accepted: 05/23/2011] [Indexed: 05/27/2023]
Abstract
Rootless aquatic carnivorous Utricularia exude up to 25% of their photosynthates into the trap lumen, which also harbours a complex microbial community thought to play a role in enhancing Utricularia nutrient acquisition. We investigated the composition of organic carbon in the trap fluid, its availability for microbial uptake, the influence of plant nutrient status and trap age on its biodegradability, and the composition of prokaryotic assemblages within the traps of three aquatic Utricularia species. Using ion chromatography and basal respiration rate measurements we confirmed that up to 30% of total dissolved organic carbon in Utricularia trap fluid in oligotrophic conditions was easily biodegradable compounds commonly found in plant root exudates (mainly glucose, fructose and lactate). The proportion of these compounds and their microbial utilisation decreased with increasing mineral nutrient supply and trap age. Fluorescence in situ hybridisation analyses showed that microbial trap assemblages are dominated by alpha and beta Proteobacteria, and that the assemblage composition is affected by changes in the ambient mineral nutrient supply. We suggest that organic carbon dynamics within the traps, involving both the plant and associated microbial assemblages, underlies the acquisition of key nutrients by Utricularia and may help explain the evolutionary success of the genus.
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Affiliation(s)
- Dagmara Sirov
- Faculty of Science, University of South Bohemia, Department of Ecosystem Biology, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Jakub Borovec
- Faculty of Science, University of South Bohemia, Department of Ecosystem Biology, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Tom X Picek
- Faculty of Science, University of South Bohemia, Department of Ecosystem Biology, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
| | - Lubom R Adamec
- Institute of Botany AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic
| | - Linda Nedbalov
- Institute of Botany AS CR, Dukelská 135, CZ-37982 Třeboň, Czech Republic
| | - Jaroslav Vrba
- Faculty of Science, University of South Bohemia, Department of Ecosystem Biology, Branišovská 31, CZ-37005 České Budějovice, Czech Republic
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21
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The carnivorous pale pitcher plant harbors diverse, distinct, and time-dependent bacterial communities. Appl Environ Microbiol 2010; 76:1851-60. [PMID: 20097807 DOI: 10.1128/aem.02440-09] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of American carnivorous pitcher plants (Sarracenia) to digest insect prey is facilitated by microbial associations. Knowledge of the details surrounding this interaction has been limited by our capability to characterize bacterial diversity in this system. To describe microbial diversity within and between pitchers of one species, Sarracenia alata, and to explore how these communities change over time as pitchers accumulate and digest insect prey, we collected and analyzed environmental sequence tag (454 pyrosequencing) and genomic fingerprint (automated ribosomal intergenic spacer analysis and terminal restriction fragment length polymorphism) data. Microbial richness associated with pitcher plant fluid is high; more than 1,000 unique phylogroups were identified across at least seven phyla and 50 families. We documented an increase in bacterial diversity and abundance with time and observed repeated changes in bacterial community composition. Pitchers from different plants harbored significantly more similar bacterial communities at a given time point than communities coming from the same genetic host over time. The microbial communities in pitcher plant fluid also differ significantly from those present in the surrounding soil. These findings indicate that the bacteria associated with pitcher plant leaves are far from random assemblages and represent an important step toward understanding this unique plant-microbe interaction.
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22
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Benata H, Mohammed O, Noureddine B, Abdelbasset B, Abdelmoumen H, Muresu R, Squartini A, El Idrissi MM. Diversity of bacteria that nodulate Prosopis juliflora in the eastern area of Morocco. Syst Appl Microbiol 2008; 31:378-86. [PMID: 18789623 DOI: 10.1016/j.syapm.2008.08.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A total of 274 bacterial strains were isolated from the root nodules of Prosopis juliflora, growing in two arid soils of the eastern area of Morocco. A physiological plate screening allowed the selection of 15 strains that could tolerate NaCl concentrations between 175 and 500 mM. These were compared with 15 strains chosen from among the ones which did not tolerate high salinity. The diversity of strains was first assessed by rep-PCR amplification fingerprinting using BOXA1R and ERIC primers. An analysis of the PCR-amplified 16S rDNA gene digestion profiles using five endonucleases indicated the presence of different lineages among the taxa associated with P. juliflora nodules in the soils studied. Nucleotide sequencing of the small subunit rRNA gene and BLAST analysis showed that P. juliflora could host at least six bacterial species in this region and that the identity of those associated with high salt tolerance was clearly distinct from that of the salt-sensitive ones. Among the former, the first type displayed 99% similarity with different members of the genus Sinorhizobium, the second 97% similarity with species within the genus Rhizobium, while the third ribosomal type had 100% homology to Achromobacter xylosoxidans. Within the salt-sensitive isolates the prevailing type observed showed 98% similarity with Rhizobium multihospitium and R. tropici, a second type had 98% similarity to R. giardinii, and a further case displayed 97% colinearity with the Ensifer group including E. maghrebium and E. xericitae. All of the thirty strains encompassing these types re-nodulated P. juliflora in microbiologically controlled conditions and all of them were shown to possess a copy of the nodC gene. This is the first report detecting the betaproteobacterial genus Achromobacter as nodule-forming species for legumes. The observed variability in symbiont species and the abundance of nodulation-proficient strains is in line with the observation that the plant always appears to be nodulated and efficiently fixing nitrogen in spite of a wide range of soil and environmental conditions.
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Affiliation(s)
- Hanane Benata
- Laboratoire de Biologie des Plantes et des Microorganismes, Faculty of Sciences, Mohamed Premier University, Oujda, Morocco
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Peterson CN, Day S, Wolfe BE, Ellison AM, Kolter R, Pringle A. A keystone predator controls bacterial diversity in the pitcher-plant (Sarracenia purpurea) microecosystem. Environ Microbiol 2008; 10:2257-66. [DOI: 10.1111/j.1462-2920.2008.01648.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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