1
|
Maosa JO, Wang S, Liu S, Li H, Qing X, Bert W. Exploring the use of metabarcoding to reveal eukaryotic associations with mononchids nematodes. J Nematol 2024; 56:20240016. [PMID: 38737093 PMCID: PMC11086744 DOI: 10.2478/jofnem-2024-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Indexed: 05/14/2024] Open
Abstract
Nematodes play a vital ecological role in soil and marine ecosystems, but there is limited information about their dietary diversity and feeding habits. Due to methodological challenges, the available information is based on inference rather than confirmed observations. The lack of correct dietary requirements also hampers rearing experiments. To achieve insight into the prey of mononchid nematodes, this study employed high-throughput Illumina paired-end sequencing using universal eukaryotic species 18S primers on 10 pooled mononchid nematode species, namely Mylonchulus brachyuris, M. brevicaudatus, Mylonchulus sp., Clarkus parvus, Prionchulus sp. M. hawaiiensis, M. sigmaturellus, M. vulvapapillatus, Anatonchus sp. and Miconchus sp. The results indicate that mononchids are associated with a remarkable diversity of eukaryotes, including fungi, algae, and protists. While the metabarcoding approach, first introduced here for mononchids, proved to be a simple and rapid method, it has several limitations and crucial methodological challenges that should be addressed in future studies. Ultimately, such methods should be able to evaluate the dietary complexity of nematodes and provide a valuable avenue for unraveling the dietary requirements of previously unculturable nematodes. This can contribute to the methodology of understanding their feeding habits and contributions to ecosystem dynamics.
Collapse
Affiliation(s)
- Joseph O. Maosa
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000Ghent, Belgium
| | - Siqi Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Shuhan Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Hongmei Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Xue Qing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000Ghent, Belgium
| |
Collapse
|
2
|
González-Pech RA, Li VY, Garcia V, Boville E, Mammone M, Kitano H, Ritchie KB, Medina M. The Evolution, Assembly, and Dynamics of Marine Holobionts. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:443-466. [PMID: 37552896 DOI: 10.1146/annurev-marine-022123-104345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The holobiont concept (i.e., multiple living beings in close symbiosis with one another and functioning as a unit) is revolutionizing our understanding of biology, especially in marine systems. The earliest marine holobiont was likely a syntrophic partnership of at least two prokaryotic members. Since then, symbiosis has enabled marine organisms to conquer all ocean habitats through the formation of holobionts with a wide spectrum of complexities. However, most scientific inquiries have focused on isolated organisms and their adaptations to specific environments. In this review, we attempt to illustrate why a holobiont perspective-specifically, the study of how numerous organisms form a discrete ecological unit through symbiosis-will be a more impactful strategy to advance our understanding of the ecology and evolution of marine life. We argue that this approach is instrumental in addressing the threats to marine biodiversity posed by the current global environmental crisis.
Collapse
Affiliation(s)
- Raúl A González-Pech
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Vivian Y Li
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Vanessa Garcia
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Elizabeth Boville
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Marta Mammone
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | | | - Kim B Ritchie
- Department of Natural Sciences, University of South Carolina, Beaufort, South Carolina, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| |
Collapse
|
3
|
Pereira TJ, Walters TL, El-Shaffey HM, Bik HM, Frischer ME. The microbiome of the pelagic tunicate Dolioletta gegenbauri: A potential link between the grazing and microbial food web. Mol Ecol 2023; 32:6564-6579. [PMID: 35989550 DOI: 10.1111/mec.16668] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/28/2022]
Abstract
Bloom-forming gelatinous zooplankton occur circumglobally and significantly influence the structure of pelagic marine food webs and biogeochemical cycling through interactions with microbial communities. During bloom conditions especially, gelatinous zooplankton are keystone taxa that help determine the fate of primary production, nutrient remineralization, and carbon export. Using the pelagic tunicate Dolioletta gegenbauri as a model system for gelatinous zooplankton, we carried out a laboratory-based feeding experiment to investigate the potential ecosystem impacts of doliolid gut microbiomes and microbial communities associated with doliolid faecal pellets and the surrounding seawater. Metabarcoding targeting Bacteria and Archaea 16S rRNA genes/Archaea) and qPCR approaches were used to characterize microbiome assemblages. Comparison between sample types revealed distinct patterns in microbial diversity and biomass that were replicable across experiments. These observations support the hypothesis that through their presence and trophic activity, doliolids influence the structure of pelagic food webs and biogeochemical cycling in subtropical continental shelf systems where tunicate blooms are common. Bacteria associated with starved doliolids (representative of the resident gut microbiome) possessed distinct low-biomass and low-diversity microbial assemblages, suggesting that the doliolid microbiome is optimized to support a detrital trophic mode. Bacterial genera Pseudoalteromomas and Shimia were the most abundant potential core microbiome taxa, similar to patterns observed in other marine invertebrates. Exploratory bioinformatic analyses of predicted functional genes suggest that doliolids, via their interactions with bacterial communities, may affect important biogeochemical processes including nitrogen, sulphur, and organic matter cycling.
Collapse
Affiliation(s)
- Tiago J Pereira
- Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Tina L Walters
- Department of Marine Sciences, University of Georgia Skidaway Institute of Oceanography, Savannah, Georgia, USA
| | - Hisham M El-Shaffey
- Department of Marine Sciences, University of Georgia Skidaway Institute of Oceanography, Savannah, Georgia, USA
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Holly M Bik
- Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Marc E Frischer
- Department of Marine Sciences, University of Georgia Skidaway Institute of Oceanography, Savannah, Georgia, USA
| |
Collapse
|
4
|
Holt CC, Dhaliwal S, Na I, Mtawali M, Boscaro V, Keeling P. Spatial compartmentalisation of bacteria in phoronid microbiomes. Sci Rep 2023; 13:18612. [PMID: 37903823 PMCID: PMC10616082 DOI: 10.1038/s41598-023-45652-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/22/2023] [Indexed: 11/01/2023] Open
Abstract
The phylum Phoronida comprises filter-feeding invertebrates that live in a protective tube sometimes reinforced with particulate material from the surrounding environments. Animals with these characteristics make promising candidate hosts for symbiotic bacteria, given the constant interactions with various bacterial colonizers, yet phoronids are one of the very few animal phyla with no available microbiome data whatsoever. Here, by sequencing the V4 region of the 16S rRNA gene, we compare bacterial microbiomes in whole phoronids, including both tube and living tissues, with those associated exclusively to the isolated tube and/or the naked animal inside. We also compare these communities with those from the surrounding water. Phoronid microbiomes from specimens belonging to the same colony but collected a month apart were significantly different, and bacterial taxa previously reported in association with invertebrates and sediment were found to drive this difference. The microbiomes associated with the tubes are very similar in composition to those isolated from whole animals. However, just over half of bacteria found in whole specimens are also found both in tubes and naked specimens. In conclusion, phoronids harbour bacterial microbiomes that differ from those in the surrounding water, but the composition of those microbiomes is not stable and appears to change in the same colony over a relatively short time frame. Considering individual spatial/anatomical compartments, the phoronid tube contributes most to the whole-animal microbiome.
Collapse
Affiliation(s)
- Corey C Holt
- Department of Botany, University of British Columbia, Vancouver, Canada.
- Hakai Institute, Heriot Bay, Canada.
| | - Sahib Dhaliwal
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Ina Na
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Mahara Mtawali
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Patrick Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada.
| |
Collapse
|
5
|
Buschi E, Dell’Anno A, Tangherlini M, Stefanni S, Lo Martire M, Núñez-Pons L, Avila C, Corinaldesi C. Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean. Front Microbiol 2023; 14:1234725. [PMID: 37799611 PMCID: PMC10548270 DOI: 10.3389/fmicb.2023.1234725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023] Open
Abstract
Microbiota plays essential roles in the health, physiology, and in adaptation of marine multi-cellular organisms to their environment. In Antarctica, marine organisms have a wide range of unique physiological functions and adaptive strategies, useful for coping with extremely cold conditions. However, the role of microbiota associated with Antarctic organisms in such adaptive strategies is underexplored. In the present study, we investigated the diversity and putative functions of the microbiome of the sea star Odontaster validus, one of the main keystone species of the Antarctic benthic ecosystems. We compared the whole-body bacterial microbiome of sea stars from different sites of the Antarctic Peninsula and Ross Sea, two areas located in two opposite geographical sectors of the Antarctic continent. The taxonomic composition of O. validus microbiomes changed both between and within the two Antarctic sectors, suggesting that environmental and biological factors acting both at large and local scales may influence microbiome diversity. Despite this, one bacterial family (Rhodobacteraceae) was shared among all sea star individuals from the two geographical sectors, representing up to 95% of the microbial core, and suggesting a key functional role of this taxon in holobiont metabolism and well-being. In addition, the genus Roseobacter belonging to this family was also present in the surrounding sediment, implying a potential horizontal acquisition of dominant bacterial core taxa via host-selection processes from the environment.
Collapse
Affiliation(s)
- Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica di Napoli “Anton Dohrn”, Fano Marine Centre, Fano, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica di Napoli “Anton Dohrn”, Fano Marine Centre, Fano, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica di Napoli “Anton Dohrn”, Naples, Italy
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology, Stazione Zoologica di Napoli “Anton Dohrn”, Naples, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Conxita Avila
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat, University of Barcelona, Barcelona, Catalonia, Spain
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
| |
Collapse
|
6
|
Parr McQueen J, Gattoni K, Gendron E, Schmidt S, Sommers P, Porazinska DL. External and Internal Microbiomes of Antarctic Nematodes are Distinct, but More Similar to each other than the Surrounding Environment. J Nematol 2023; 55:20230004. [PMID: 36969543 PMCID: PMC10035304 DOI: 10.2478/jofnem-2023-0004] [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: 08/02/2022] [Indexed: 03/11/2023] Open
Abstract
Host-associated microbiomes have primarily been examined in the context of their internal microbial communities, but many animal species also contain microorganisms on external host surfaces that are important to host physiology. For nematodes, single strains of bacteria are known to adhere to the cuticle (e.g., Pasteuria penetrans), but the structure of a full external microbial community is uncertain. In prior research, we showed that internal gut microbiomes of nematodes (Plectus murrayi, Eudorylaimus antarcticus) and tardigrades from Antarctica's McMurdo Dry Valleys were distinct from the surrounding environment and primarily driven by host identity. Building on this work, we extracted an additional set of individuals containing intact external microbiomes and amplified them for 16S and 18S rRNA metabarcoding. Our results showed that external bacterial microbiomes were more diverse than internal microbiomes, but less diverse than the surrounding environment. Host-specific bacterial compositional patterns were observed, and external microbiomes were most similar to their respective internal microbiomes. However, external microbiomes were more influenced by the environment than the internal microbiomes were. Non-host eukaryotic communities were similar in diversity to internal eukaryotic communities, but exhibited more stochastic patterns of assembly compared to bacterial communities, suggesting the lack of a structured external eukaryotic microbiome. Altogether, we provide evidence that nematode and tardigrade cuticles are inhabited by robust bacterial communities that are substantially influenced by the host, albeit less so than internal microbiomes are.
Collapse
Affiliation(s)
- J. Parr McQueen
- Department of Entomology and Nematology, University of Florida, FL 32611FloridaUSA
| | - K. Gattoni
- Department of Entomology and Nematology, University of Florida, FL 32611FloridaUSA
| | - E.M.S. Gendron
- Department of Entomology and Nematology, University of Florida, FL 32611FloridaUSA
| | - S.K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO 80309Colorado BoulderUSA
| | - P. Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO 80309Colorado BoulderUSA
| | - D. L. Porazinska
- Department of Entomology and Nematology, University of Florida, FL 32611FloridaUSA
| |
Collapse
|
7
|
Ramalho MO, Moreau CS. Untangling the complex interactions between turtle ants and their microbial partners. Anim Microbiome 2023; 5:1. [PMID: 36597141 PMCID: PMC9809061 DOI: 10.1186/s42523-022-00223-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/20/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND To understand the patterns of biodiversity it is important to consider symbiotic interactions as they can shape animal evolution. In several ant genera symbiotic interactions with microbial communities have been shown to have profound impacts for the host. For example, we know that for Camponotini the gut community can upgrade the host's diet and is shaped by development and colony interactions. However, what is true for one ant group may not be true for another. For the microbial communities that have been examined across ants we see variation in the diversity, host factors that structure these communities, and the function these microbes provide for the host. In the herbivorous turtle ants (Cephalotes) their stable symbiotic interactions with gut bacteria have persisted for 50 million years with the gut bacteria synthesizing essential amino acids that are used by the host. Although we know the function for some of these turtle ant-associated bacteria there are still many open questions. RESULTS In the present study we examined microbial community diversity (16S rRNA and 18S rRNA amplicons) of more than 75 species of turtle ants across different geographic locations and in the context of the host's phylogenetic history. Our results show (1) that belonging to a certain species and biogeographic regions are relevant to structuring the microbial community of turtle ants; (2) both bacterial and eukaryotic communities demonstrated correlations and cooccurrence within the ant host; (3) within the core bacterial community, Burkholderiaceae bacterial lineage were the only group that showed strong patterns of codiversification with the host, which is remarkable since the core bacterial community is stable and persistent. CONCLUSIONS We concluded that for the turtle ants there is a diverse and evolutionarily stable core bacterial community, which leads to interesting questions about what microbial or host factors influence when these partner histories become evolutionarily intertwined.
Collapse
Affiliation(s)
- Manuela O. Ramalho
- grid.268132.c0000 0001 0701 2416Department of Biology, West Chester University, 750 South Church Street, West Chester, PA 19383 USA
| | - Corrie S. Moreau
- grid.5386.8000000041936877XDepartment of Entomology, Cornell University, Ithaca, NY 14853 USA ,grid.5386.8000000041936877XDepartment of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853 USA
| |
Collapse
|
8
|
McQueen JP, Gattoni K, Gendron EMS, Schmidt SK, Sommers P, Porazinska DL. Host identity is the dominant factor in the assembly of nematode and tardigrade gut microbiomes in Antarctic Dry Valley streams. Sci Rep 2022; 12:20118. [PMID: 36446870 PMCID: PMC9709161 DOI: 10.1038/s41598-022-24206-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/11/2022] [Indexed: 11/30/2022] Open
Abstract
Recent work examining nematode and tardigrade gut microbiomes has identified species-specific relationships between host and gut community composition. However, only a handful of species from either phylum have been examined. How microbiomes differ among species and what factors contribute to their assembly remains unexplored. Cyanobacterial mats within Antarctic Dry Valley streams host a simple and tractable natural ecosystem of identifiable microinvertebrates to address these questions. We sampled 2 types of coexisting mats (i.e., black and orange) across four spatially isolated streams, hand-picked single individuals of two nematode species (i.e., Eudorylaimus antarcticus and Plectus murrayi) and tardigrades, to examine their gut microbiomes using 16S and 18S rRNA metabarcoding. All gut microbiomes (bacterial and eukaryotic) were significantly less diverse than the mats they were isolated from. In contrast to mats, microinvertebrates' guts were depleted of Cyanobacteria and differentially enriched in taxa of Bacteroidetes, Proteobacteria, and Fungi. Among factors investigated, gut microbiome composition was most influenced by host identity while environmental factors (e.g., mats and streams) were less important. The importance of host identity in predicting gut microbiome composition suggests functional value to the host, similar to other organisms with strong host selected microbiomes.
Collapse
Affiliation(s)
- J. Parr McQueen
- grid.15276.370000 0004 1936 8091Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611 USA
| | - Kaitlin Gattoni
- grid.15276.370000 0004 1936 8091Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611 USA
| | - Eli M. S. Gendron
- grid.15276.370000 0004 1936 8091Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611 USA
| | - Steven K. Schmidt
- grid.266190.a0000000096214564Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
| | - Pacifica Sommers
- grid.266190.a0000000096214564Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
| | - Dorota L. Porazinska
- grid.15276.370000 0004 1936 8091Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611 USA
| |
Collapse
|
9
|
Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis. Nat Microbiol 2022; 7:810-819. [PMID: 35618773 DOI: 10.1038/s41564-022-01125-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 04/12/2022] [Indexed: 01/02/2023]
Abstract
Animals and microorganisms often establish close ecological relationships. However, much of our knowledge about animal microbiomes comes from two deeply studied groups: vertebrates and arthropods. To understand interactions on a broader scale of diversity, we characterized the bacterial microbiomes of close to 1,000 microscopic marine invertebrates from 21 phyla, spanning most of the remaining tree of metazoans. Samples were collected from five temperate and tropical locations covering three marine habitats (sediment, water column and intertidal macroalgae) and bacterial microbiomes were characterized using 16S ribosomal RNA gene sequencing. Our data show that, despite their size, these animals harbour bacterial communities that differ from those in the surrounding environment. Distantly related but coexisting invertebrates tend to share many of the same bacteria, suggesting that guilds of microorganisms preferentially associated with animals, but not tied to any specific host lineage, are the main drivers of the ecological relationship. Host identity is a minor factor shaping these microbiomes, which do not show the same correlation with host phylogeny, or 'phylosymbiosis', observed in many large animals. Hence, the current debate on the varying strength of phylosymbiosis within selected lineages should be reframed to account for the possibility that such a pattern might be the exception rather than the rule.
Collapse
|
10
|
Kanfra X, Wrede A, Moll J, Heuer H. Nematode-Microbe Complexes in Soils Replanted with Apple. Microorganisms 2022; 10:microorganisms10010157. [PMID: 35056606 PMCID: PMC8780120 DOI: 10.3390/microorganisms10010157] [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: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 02/01/2023] Open
Abstract
Apple replant disease is a severe problem in orchards and tree nurseries. Evidence for the involvement of a nematode–microbe disease complex was reported. To search for this complex, plots with a history of apple replanting, and control plots cultivated for the first time with apple were sampled in two fields in two years. Shoot weight drastically decreased with each replanting. Amplicon sequencing of the nematode community and co-extracted fungal and bacterial communities revealed significant differences between replanted and control plots. Free-living nematodes of the genera Aphelenchus and Cephalenchus and an unidentified Dorylaimida were associated with replanted plots, as indicated by linear discriminant analysis effect size. Among the co-extracted fungi and bacteria, Mortierella and Methylotenera were most indicative of replanting. Some genera, mostly Rhabditis, Streptomyces and a fungus belonging to the Chaetomiaceae indicated healthy control plots. Isolating and investigating the putative disease complexes will help to understand and alleviate stress-induced root damage of apple in replanted soil.
Collapse
Affiliation(s)
- Xorla Kanfra
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany;
| | - Andreas Wrede
- Department of Horticulture, Landwirtschaftskammer Schleswig-Holstein, 25373 Ellerhoop, Germany;
| | - Julia Moll
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany;
| | - Holger Heuer
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany;
- Correspondence:
| |
Collapse
|
11
|
Kashinskaya EN, Simonov EP, Vlasenko PG, Markevich GN, Shokurova AV, Andree KB, Solovyev MM. The gut microbiota of Cystidicola farionis parasitizing the swim bladder of the nosed charr morph Salvelinus malma complex in Lake Kronotskoe (Kamchatka, Russia). J Nematol 2021; 53:e2021-106. [PMID: 34957411 PMCID: PMC8672423 DOI: 10.21307/jofnem-2021-106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 12/23/2022] Open
Abstract
Using the approach of sequencing the V3–V4 region of the 16S rRNA gene, we have analyzed the bacterial diversity associated with the gut and “body” (other parts of nematode after dissection: cuticle, epidermis and longitudinal muscles, etc) of Cystidicola farionis parasitizing the swim bladder of different morphotypes of the nosed charr. Comparisons of the gut microbiota of nematodes with their “body” has revealed that the associated microbiota are closely related to each other. Taxonomic analysis indicated that the relative abundances of the dominant nematode-associated bacteria varied with individual fish. The common dominant microbiota of the gut and “body” of nematodes were represented by Aeromonas, Pseudomonas, Shewanella, and Yersinia, while the associated microbiota of the swim bladder of the nosed charr was dominated by Acinetobacter, Cetobacterium, Pajaroellobacter, Paracoccus, Pseudomonas, Shewanella. By comparing the associated microbiota of nematode parasitizing the different morphotypes of the nosed charr the difference in richness estimates (number of OTU’s and Chao1) were revealed between the N1g and N2 morphs.
Collapse
Affiliation(s)
- E N Kashinskaya
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia
| | - E P Simonov
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia.,University of Tyumen, Institute of Environmental and Agricultural Biology (X-BIO), 25 Lenina St., Tyumen, 625003, Russia
| | - P G Vlasenko
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia
| | | | - A V Shokurova
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia
| | - K B Andree
- Instituto de Investigación y Tecnología Agroalimentarias; Cultius Aquàtics; San Carlos de la Rapita, Tarragona, ES 08140, Spain
| | - M M Solovyev
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia.,Tomsk State University; Institute of Biology, Ecology, Soil Science, Agriculture, and Forestry; 36 Lenin Ave, Tomsk, 634050, Russia
| |
Collapse
|
12
|
Albert S, Hedberg P, Motwani NH, Sjöling S, Winder M, Nascimento FJA. Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities. Sci Rep 2021; 11:24033. [PMID: 34911983 PMCID: PMC8674317 DOI: 10.1038/s41598-021-03303-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/30/2021] [Indexed: 11/10/2022] Open
Abstract
In coastal aphotic sediments, organic matter (OM) input from phytoplankton is the primary food resource for benthic organisms. Current observations from temperate ecosystems like the Baltic Sea report a decline in spring bloom diatoms, while summer cyanobacteria blooms are becoming more frequent and intense. These climate-driven changes in phytoplankton communities may in turn have important consequences for benthic biodiversity and ecosystem functions, but such questions are not yet sufficiently explored experimentally. Here, in a 4-week experiment, we investigated the response of microeukaryotic and bacterial communities to different types of OM inputs comprising five ratios of two common phytoplankton species in the Baltic Sea, the diatom Skeletonema marinoi and filamentous cyanobacterium Nodularia spumigena. Metabarcoding analyses on 16S and 18S ribosomal RNA (rRNA) at the experiment termination revealed subtle but significant changes in diversity and community composition of microeukaryotes in response to settling OM quality. Sediment bacteria were less affected, although we observed a clear effect on denitrification gene expression (nirS and nosZ), which was positively correlated with increasing proportions of cyanobacteria. Altogether, these results suggest that future changes in OM input to the seafloor may have important effects on both the composition and function of microbenthic communities.
Collapse
Affiliation(s)
- Séréna Albert
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius 20A, 106 91, Stockholm, Sweden.
| | - Per Hedberg
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius 20A, 106 91, Stockholm, Sweden
| | - Nisha H Motwani
- Department of Environmental Science, School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Sara Sjöling
- Department of Environmental Science, School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Monika Winder
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius 20A, 106 91, Stockholm, Sweden
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius 20A, 106 91, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| |
Collapse
|
13
|
Potential impacts of polymetallic nodule removal on deep-sea meiofauna. Sci Rep 2021; 11:19996. [PMID: 34620971 PMCID: PMC8497503 DOI: 10.1038/s41598-021-99441-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/17/2021] [Indexed: 11/17/2022] Open
Abstract
Deep seabed mining is potentially imminent in the Clarion Clipperton Fracture Zone (CCFZ; northeast Pacific). Seabed collectors will remove polymetallic nodules and the surrounding surface sediments, both inhabited by meiofauna, along their path. To determine potential impacts of polymetallic nodule removal, we investigated the importance of nodule presence for the abundance, composition and diversity of sediment meiofauna, and evaluated the existence and composition of nodule crevice meiofauna in the Global Sea Mineral Resources (GSR) exploration contract area. Nodule-free and nodule-rich sediments displayed high biodiversity with many singletons and doubletons, potentially representing rare taxa. Nodule presence negatively influenced sediment meiofaunal abundances but did not markedly affect taxonomic composition or diversity. This is the first report on CCFZ nodule crevice meiofauna, whose abundance related positively to nodule dimensions. Though dominated by the same taxa, nodules and sediments differed regarding the taxonomic and trophic composition of the meio- and nematofauna. Nevertheless, there were no taxa endemic to the nodule crevices and nodule crevice meiofauna added only little to total small-scale (~ cm) meiofaunal abundance and diversity. We formulated environmental management recommendations at the contract area and regional (CCFZ) scale related to sampling effort, set-aside preservation and monitoring areas, and potential rehabilitation measures.
Collapse
|
14
|
Sevigny JL, Norenburg JL, Leasi F. A Bioinformatics Tutorial for Comparative Development Genomics in Diverse Meiofauna. Methods Mol Biol 2021; 2219:289-305. [PMID: 33074549 DOI: 10.1007/978-1-0716-0974-3_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Miniaturization, which is a common feature in animals, is particularly manifest in meiofauna-animals sharing peculiar phenotypic features that evolved as adaptations to the highly specialized aquatic interstitial habitat. While revealing much about the extreme phyletic diversity of meiofauna, the genome structure of meiofaunal species could also characterize the phenotype of ancestral states as well as explain the origin and evolution of miniaturization. Here, we present a practical bioinformatics tutorial for genome assembly, genome comparison, and characterization of Hox clusters in meiofaunal species.
Collapse
Affiliation(s)
- Joseph L Sevigny
- Hubbard Center for Genome Studies, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Jon L Norenburg
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Francesca Leasi
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN, USA.
| |
Collapse
|
15
|
Bellec L, Cambon-Bonavita MA, Durand L, Aube J, Gayet N, Sandulli R, Brandily C, Zeppilli D. Microbial Communities of the Shallow-Water Hydrothermal Vent Near Naples, Italy, and Chemosynthetic Symbionts Associated With a Free-Living Marine Nematode. Front Microbiol 2020; 11:2023. [PMID: 32973733 PMCID: PMC7469538 DOI: 10.3389/fmicb.2020.02023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/30/2020] [Indexed: 11/17/2022] Open
Abstract
Shallow-water hydrothermal vents are widespread, especially in the Mediterranean Sea, owing to the active volcanism of the area. Apart free microbial communities’ investigations, few biological studies have been leaded yet. Investigations of microbial communities associated with Nematoda, an ecologically important group in sediments, can help to improve our overall understanding of these ecosystems. We used a multidisciplinary-approach, based on microscopic observations (scanning electron microscopy: SEM and Fluorescence In Situ Hybridization: FISH) coupled with a molecular diversity analysis using metabarcoding, based on the 16S rRNA gene (V3-V4 region), to characterize the bacterial community of a free-living marine nematode and its environment, the shallow hydrothermal vent near Naples (Italy). Observations of living bacteria in the intestine (FISH), molecular and phylogenetic analyses showed that this species of nematode harbors its own bacterial community, distinct from the surrounding sediment and water. Metabarcoding results revealed the specific microbiomes of the sediment from three sites of this hydrothermal area to be composed mainly of sulfur oxidizing and reducing related bacteria.
Collapse
Affiliation(s)
- Laure Bellec
- Ifremer, Centre Brest, REM/EEP/LEP, ZI de la Pointe du Diable, CS10070, Plouzané, France.,Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, Plouzané, France.,EPOC, UMR 5805, University of Bordeaux, Arcachon, France
| | | | - Lucile Durand
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, Plouzané, France
| | - Johanne Aube
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, Plouzané, France
| | - Nicolas Gayet
- Ifremer, Centre Brest, REM/EEP/LEP, ZI de la Pointe du Diable, CS10070, Plouzané, France
| | - Roberto Sandulli
- Laboratory of Marine Ecology, Department of Science and Technology, University of Naples "Parthenope," Naples, Italy
| | - Christophe Brandily
- Ifremer, Centre Brest, REM/EEP/LEP, ZI de la Pointe du Diable, CS10070, Plouzané, France
| | - Daniela Zeppilli
- Ifremer, Centre Brest, REM/EEP/LEP, ZI de la Pointe du Diable, CS10070, Plouzané, France
| |
Collapse
|
16
|
Development but not diet alters microbial communities in the Neotropical arboreal trap jaw ant Daceton armigerum: an exploratory study. Sci Rep 2020; 10:7350. [PMID: 32355187 PMCID: PMC7192945 DOI: 10.1038/s41598-020-64393-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/31/2020] [Indexed: 01/01/2023] Open
Abstract
To better understand the evolutionary significance of symbiotic interactions in nature, microbiome studies can help to identify the ecological factors that may shape host-associated microbial communities. In this study we explored both 16S and 18S rRNA microbial communities of D. armigerum from both wild caught individuals collected in the Amazon and individuals kept in the laboratory and fed on controlled diets. We also investigated the role of colony, sample type, development and caste on structuring microbial communities. Our bacterial results (16S rRNA) reveal that (1) there are colony level differences between bacterial communities; (2) castes do not structure communities; (3) immature stages (brood) have different bacterial communities than adults; and 4) individuals kept in the laboratory with a restricted diet showed no differences in their bacterial communities from their wild caught nest mates, which could indicate the presence of a stable and persistent resident bacterial community in this host species. The same categories were also tested for microbial eukaryote communities (18S rRNA), and (5) developmental stage has an influence on the diversity recovered; (6) the diversity of taxa recovered has shown this can be an important tool to understand additional aspects of host biology and species interactions.
Collapse
|
17
|
Adair KL, Bost A, Bueno E, Kaunisto S, Kortet R, Peters-Schulze G, Martinson VG, Douglas AE. Host determinants of among-species variation in microbiome composition in drosophilid flies. THE ISME JOURNAL 2020; 14:217-229. [PMID: 31624341 PMCID: PMC6908599 DOI: 10.1038/s41396-019-0532-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/08/2019] [Accepted: 09/24/2019] [Indexed: 12/18/2022]
Abstract
The taxonomic composition of microbial communities in animals varies among animal species, but the contribution of interspecific differences in filtering of the microbial pool by the animal host to this variation is uncertain. Here, we demonstrate significant interspecific variation in microbial community composition among laboratory-reared Drosophila species that was not related to host phylogeny. Complementary reciprocal transfer experiments yielded different microbial communities for a single microbiota administered to homologous and heterologous hosts (i.e., the same and different Drosophila species from which the microbiota was derived), indicative of among-host species differences in traits that shape microbiota composition. The difference in microbiota composition between homologous and heterologous hosts was not greater for distantly related than for closely related host species pairs. Furthermore, Drosophila survival to adulthood was significantly reduced in heterologous associations relative to homologous associations and microbiologically sterile flies, suggesting that microbial taxa that are advantageous for their homologous host species can be deleterious for other host species. We conclude that drosophilid flies display robust among-host species variation in host controls over microbiota composition that has diversified in response to selection pressures which are not tracked by host phylogeny.
Collapse
Affiliation(s)
- Karen L Adair
- Department of Entomology, Cornell University, Ithaca, NY, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Alyssa Bost
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Eduardo Bueno
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Sirpa Kaunisto
- Department of Biology, University of Western Ontario, London, ON, Canada
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Raine Kortet
- Department of Biology, University of Western Ontario, London, ON, Canada
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | | | - Vincent G Martinson
- Department of Biology, University of Rochester, Rochester, NY, USA
- Department of Entomology, University of Georgia, Athens, GA, 30602, USA
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, NY, USA.
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
18
|
Nascimento FJA, Dahl M, Deyanova D, Lyimo LD, Bik HM, Schuelke T, Pereira TJ, Björk M, Creer S, Gullström M. Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure. Commun Biol 2019; 2:362. [PMID: 31602411 PMCID: PMC6778119 DOI: 10.1038/s42003-019-0610-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/12/2019] [Indexed: 11/08/2022] Open
Abstract
Ecological interactions between aquatic plants and sediment communities can shape the structure and function of natural systems. Currently, we do not fully understand how seagrass habitat degradation impacts the biodiversity of belowground sediment communities. Here, we evaluated indirect effects of disturbance of seagrass meadows on meiobenthic community composition, with a five-month in situ experiment in a tropical seagrass meadow. Disturbance was created by reducing light availability (two levels of shading), and by mimicking grazing events (two levels) to assess impacts on meiobenthic diversity using high-throughput sequencing of 18S rRNA amplicons. Both shading and simulated grazing had an effect on meiobenthic community structure, mediated by seagrass-associated biotic drivers and sediment abiotic variables. Additionally, shading substantially altered the trophic structure of the nematode community. Our findings show that degradation of seagrass meadows can alter benthic community structure in coastal areas with potential impacts to ecosystem functions mediated by meiobenthos in marine sediments.
Collapse
Affiliation(s)
| | - Martin Dahl
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Diana Deyanova
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Liberatus D. Lyimo
- School of Biological Sciences, University of Dodoma, Box 338, Dodoma, Tanzania
| | - Holly M. Bik
- Department of Nematology, University of California—Riverside, 900 University Avenue, Riverside, CA 92521 USA
| | - Taruna Schuelke
- Department of Nematology, University of California—Riverside, 900 University Avenue, Riverside, CA 92521 USA
| | - Tiago José Pereira
- Department of Nematology, University of California—Riverside, 900 University Avenue, Riverside, CA 92521 USA
| | - Mats Björk
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, LL57 2UW UK
| | - Martin Gullström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| |
Collapse
|
19
|
Zheng F, Zhu D, Giles M, Daniell T, Neilson R, Zhu YG, Yang XR. Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 680:70-78. [PMID: 31100670 DOI: 10.1016/j.scitotenv.2019.04.384] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Although the effects of fertilization on the abundance and diversity of soil nematodes have been widely studied, the impact of fertilization on soil nematode microbiomes remains largely unknown. Here, we investigated how different fertilizers: no fertilizer, mineral fertilizer, clean slurry (pig manure with a reduced antibiotic burden) and dirty slurry (pig manure with antibiotics) affect the microbiome of a dominant soil nematode and its associated antibiotic resistance genes (ARGs). The results of 16S rRNA gene high throughput sequencing showed that the microbiome of the soil nematode Dorylaimus stagnalis is diverse (Shannon index: 9.95) and dominated by Proteobacteria (40.3%). Application of mineral fertilizers significantly reduced the diversity of the nematode microbiome (by 28.2%; P < 0.05) but increased the abundance of Proteobacteria (by 70.1%; P = 0.001). Microbial community analysis, using a null hypothesis model, indicated that microbiomes associated with the nematode are not neutrally assembled. Organic fertilizers also altered the diversity of the nematode microbiome, but had no impact on its composition as illustrated by principal coordinates analysis (PCoA). Interestingly, although no change of total ARGs was observed in the nematode microbiome and no significant relationship existed between nematode microbiome and resistome, the abundance of 48 out of a total of 75 ARGs was enriched in the organic fertilizer treatments. Thus, the data suggests that ARGs in the nematode microbiome still had a risk of horizontal gene transfer under fertilization and nematodes might be a potential refuge for ARGs.
Collapse
Affiliation(s)
- Fei Zheng
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Madeline Giles
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Tim Daniell
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK; Department of Animal and Plant Sciences, The University of Sheffield, Sheffield S10 2TN, UK
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
| |
Collapse
|
20
|
van der Heijden LH, Graeve M, Asmus R, Rzeznik-Orignac J, Niquil N, Bernier Q, Guillou G, Asmus H, Lebreton B. Trophic importance of microphytobenthos and bacteria to meiofauna in soft-bottom intertidal habitats: A combined trophic marker approach. MARINE ENVIRONMENTAL RESEARCH 2019; 149:50-66. [PMID: 31153060 DOI: 10.1016/j.marenvres.2019.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/22/2019] [Accepted: 05/20/2019] [Indexed: 06/09/2023]
Abstract
Meiofauna can play an important role in the carbon fluxes of soft-bottom coastal habitats. Investigation of their feeding behavior and trophic position remains challenging due to their small size. In this study, we determine and compare the food sources used by nematodes and benthic copepods by using stable isotope compositions, fatty acid profiles and compound specific isotope analyses of fatty acids in the mudflats, seagrass beds and a sandflat of the Marennes-Oléron Bay, France, and the Sylt-Rømø Bight, Germany. Suspended particulate organic matter was much more 13C-depleted than other food sources and meiofauna, highlighting its poor role in the different studied habitats. The very low proportions of vascular plant fatty acid markers in meiofauna demonstrated that these consumers did not rely on this food source, either fresh or detrital, even in seagrass beds. The combined use of stable isotopes and fatty acids emphasized microphytobenthos and benthic bacteria as the major food sources of nematodes and benthic copepods. Compound specific analyses of a bacteria marker confirmed that bacteria mostly used microphytobenthos as a substrate.
Collapse
Affiliation(s)
- L H van der Heijden
- UMR 7266 Littoral, Environment et Societies (CNRS - University of La Rochelle), Institute du littoral et de l'environnement, 2 rue Olympe de Gouges, 17000, La Rochelle, France; Alfred Wegener Institute Helmholtz Centre for Polar- and Marine Research, Wattenmeerstation Sylt, Hafenstraße 43, 25992, List, Sylt, Germany.
| | - M Graeve
- Alfred Wegener Institut Helmholtz Centre for Polar- and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - R Asmus
- Alfred Wegener Institute Helmholtz Centre for Polar- and Marine Research, Wattenmeerstation Sylt, Hafenstraße 43, 25992, List, Sylt, Germany
| | - J Rzeznik-Orignac
- UMR 8222 Laboratoire d'Ecogéochimie des Environnements Benthiques, (CNRS - Sorbonne Université), Observatoire Océanologique de Banyuls, 1 avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - N Niquil
- UMR 7208 Unité Biologie des Organismes et Ecosystèmes Aquatiques (MNHN - CNRS - IRD - Sorbonne Université - Université de Caen Normandie - Université des Antilles), Esplanade de la Paix, 14000, CAEN, France
| | - Q Bernier
- UMR 7266 Littoral, Environment et Societies (CNRS - University of La Rochelle), Institute du littoral et de l'environnement, 2 rue Olympe de Gouges, 17000, La Rochelle, France
| | - G Guillou
- UMR 7266 Littoral, Environment et Societies (CNRS - University of La Rochelle), Institute du littoral et de l'environnement, 2 rue Olympe de Gouges, 17000, La Rochelle, France
| | - H Asmus
- Alfred Wegener Institute Helmholtz Centre for Polar- and Marine Research, Wattenmeerstation Sylt, Hafenstraße 43, 25992, List, Sylt, Germany
| | - B Lebreton
- UMR 7266 Littoral, Environment et Societies (CNRS - University of La Rochelle), Institute du littoral et de l'environnement, 2 rue Olympe de Gouges, 17000, La Rochelle, France
| |
Collapse
|
21
|
Hogan G, Walker S, Turnbull F, Curiao T, Morrison AA, Flores Y, Andrews L, Claesson MJ, Tangney M, Bartley DJ. Microbiome analysis as a platform R&D tool for parasitic nematode disease management. ISME JOURNAL 2019; 13:2664-2680. [PMID: 31239540 DOI: 10.1038/s41396-019-0462-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/06/2019] [Accepted: 06/06/2019] [Indexed: 12/16/2022]
Abstract
The relationship between bacterial communities and their host is being extensively investigated for the potential to improve the host's health. Little is known about the interplay between the microbiota of parasites and the health of the infected host. Using nematode co-infection of lambs as a proof-of-concept model, the aim of this study was to characterise the microbiomes of nematodes and that of their host, enabling identification of candidate nematode-specific microbiota member(s) that could be exploited as drug development tools or for targeted therapy. Deep sequencing techniques were used to elucidate the microbiomes of different life stages of two parasitic nematodes of ruminants, Haemonchus contortus and Teladorsagia circumcincta, as well as that of the co-infected ovine hosts, pre- and post infection. Bioinformatic analyses demonstrated significant differences between the composition of the nematode and ovine microbiomes. The two nematode species also differed significantly. The data indicated a shift in the constitution of the larval nematode microbiome after exposure to the ovine microbiome, and in the ovine intestinal microbial community over time as a result of helminth co-infection. Several bacterial species were identified in nematodes that were absent from their surrounding abomasal environment, the most significant of which included Escherichia coli/Shigella. The ability to purposefully infect nematode species with engineered E. coli was demonstrated in vitro, validating the concept of using this bacterium as a nematode-specific drug development tool and/or drug delivery vehicle. To our knowledge, this is the first description of the concept of exploiting a parasite's microbiome for drug development and treatment purposes.
Collapse
Affiliation(s)
- Glenn Hogan
- SynBioCentre, University College Cork, Cork, Ireland.,Cancer Research@UCC, University College Cork, Cork, Ireland
| | - Sidney Walker
- SynBioCentre, University College Cork, Cork, Ireland.,Cancer Research@UCC, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Microbiology, University College Cork, Cork, Ireland
| | - Frank Turnbull
- Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK
| | - Tania Curiao
- SynBioCentre, University College Cork, Cork, Ireland.,Cancer Research@UCC, University College Cork, Cork, Ireland
| | - Alison A Morrison
- Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK
| | - Yensi Flores
- SynBioCentre, University College Cork, Cork, Ireland.,Cancer Research@UCC, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Leigh Andrews
- Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK
| | - Marcus J Claesson
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Microbiology, University College Cork, Cork, Ireland
| | - Mark Tangney
- SynBioCentre, University College Cork, Cork, Ireland. .,Cancer Research@UCC, University College Cork, Cork, Ireland. .,APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | - Dave J Bartley
- Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK.
| |
Collapse
|
22
|
Abstract
Microbial metazoa inhabit a certain “Goldilocks zone,” where conditions are just right for the continued ignorance of these taxa. These microscopic animal species have body sizes of <1 mm and include diverse groups such as nematodes, tardigrades, kinorhynchs, loriciferans, and platyhelminths. Microbial metazoa inhabit a certain “Goldilocks zone,” where conditions are just right for the continued ignorance of these taxa. These microscopic animal species have body sizes of <1 mm and include diverse groups such as nematodes, tardigrades, kinorhynchs, loriciferans, and platyhelminths. The majority of species are too large to be considered in single-cell genomics approaches, yet too small to be wrapped into international genome sequencing initiatives. Other microbial eukaryote groups (namely the fungal and protist communities) have gained significant momentum in recent years, driven by a strong community of researchers united behind a common goal of culturing and sequencing new representatives. However, due to historical factors and difficult taxonomy, persistent research silos still exist for most microbial metazoan groups, and public molecular databases remain sparsely populated. Here, I argue that small metazoa should be embraced as a key component of microbial ecology studies, promoting a holistic and cutting-edge view of natural ecosystems.
Collapse
|
23
|
Chronopoulou PM, Salonen I, Bird C, Reichart GJ, Koho KA. Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera. Front Microbiol 2019; 10:1169. [PMID: 31191490 PMCID: PMC6547873 DOI: 10.3389/fmicb.2019.01169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/07/2019] [Indexed: 12/29/2022] Open
Abstract
Foraminifera are ubiquitous marine protists with an important role in the benthic carbon cycle. However, morphological observations often fail to resolve their exact taxonomic placement and there is a lack of field studies on their particular trophic preferences. Here, we propose the application of metabarcoding as a tool for the elucidation of the in situ feeding behavior of benthic foraminifera, while also allowing the correct taxonomic assignment of the feeder, using the V9 region of the 18S (small subunit; SSU) rRNA gene. Living foraminiferal specimens were collected from two intertidal mudflats of the Wadden Sea and DNA was extracted from foraminiferal individuals and from the surrounding sediments. Molecular analysis allowed us to confirm that our foraminiferal specimens belong to three genetic types: Ammonia sp. T6, Elphidium sp. S5 and Haynesina sp. S16. Foraminiferal intracellular eukaryote communities reflected to an extent those of the surrounding sediments but at different relative abundances. Unlike sediment eukaryote communities, which were largely determined by the sampling site, foraminiferal intracellular eukaryote communities were driven by foraminiferal species, followed by sediment depth. Our data suggests that Ammonia sp. T6 can predate on metazoan classes, whereas Elphidium sp. S5 and Haynesina sp. S16 are more likely to ingest diatoms. These observations, alongside the use of metabarcoding in similar ecological studies, significantly contribute to our overall understanding of the ecological roles of these protists in intertidal benthic environments and their position and function in the benthic food webs.
Collapse
Affiliation(s)
- Panagiota-Myrsini Chronopoulou
- Aquatic Biogeochemistry Research Unit, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Iines Salonen
- Aquatic Biogeochemistry Research Unit, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Clare Bird
- Biological and Environmental Sciences, University of Stirling, Stirling, United Kingdom
| | - Gert-Jan Reichart
- Department of Ocean Systems, NIOZ-Royal Netherlands Institute for Sea Research and Utrecht University, Den Burg, Netherlands
| | - Karoliina A Koho
- Aquatic Biogeochemistry Research Unit, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|
24
|
Chemosynthetic ectosymbionts associated with a shallow-water marine nematode. Sci Rep 2019; 9:7019. [PMID: 31065037 PMCID: PMC6505526 DOI: 10.1038/s41598-019-43517-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/02/2019] [Indexed: 12/26/2022] Open
Abstract
Prokaryotes and free-living nematodes are both very abundant and co-occur in marine environments, but little is known about their possible association. Our objective was to characterize the microbiome of a neglected but ecologically important group of free-living benthic nematodes of the Oncholaimidae family. We used a multi-approach study based on microscopic observations (Scanning Electron Microscopy and Fluorescence In Situ Hybridization) coupled with an assessment of molecular diversity using metabarcoding based on the 16S rRNA gene. All investigated free-living marine nematode specimens harboured distinct microbial communities (from the surrounding water and sediment and through the seasons) with ectosymbiosis seemed more abundant during summer. Microscopic observations distinguished two main morphotypes of bacteria (rod-shaped and filamentous) on the cuticle of these nematodes, which seemed to be affiliated to Campylobacterota and Gammaproteobacteria, respectively. Both ectosymbionts belonged to clades of bacteria usually associated with invertebrates from deep-sea hydrothermal vents. The presence of the AprA gene involved in sulfur metabolism suggested a potential for chemosynthesis in the nematode microbial community. The discovery of potential symbiotic associations of a shallow-water organism with taxa usually associated with deep-sea hydrothermal vents, is new for Nematoda, opening new avenues for the study of ecology and bacterial relationships with meiofauna.
Collapse
|
25
|
Rieseberg L, Geraldes A, Belkin SE, Chambers KE, Kane N. Editorial 2019. Mol Ecol 2019; 28:1-28. [DOI: 10.1111/mec.14976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
26
|
D'Hondt AS, Stock W, Blommaert L, Moens T, Sabbe K. Nematodes stimulate biomass accumulation in a multispecies diatom biofilm. MARINE ENVIRONMENTAL RESEARCH 2018; 140:78-89. [PMID: 29891387 DOI: 10.1016/j.marenvres.2018.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
While the effects of abiotic parameters on microbial tidal biofilms are relatively well-documented, the effects of grazing and/or bioturbation by meiofauna are poorly understood. We investigated the impact of a natural nematode assemblage on the biomass and microbial community structure of a multispecies diatom biofilm. Nematodes stimulated diatom biomass accumulation of the biofilm and caused a shift in diatom community structure. Higher diatom biomass accumulation in the presence of nematodes could be the result of increased diatom biomass production through nutrient regeneration resulting from grazing or bioturbation, and/or through shifts in interspecific interactions between diatoms (e.g. competition) through selective grazing. Alternatively, lower biomass in the controls may be due to higher secretion of diatom production in the form of bound extracellular polymeric substances (EPS). Our observations underscore that meiobenthos, and especially nematodes, are important for the structure and production of tidal biofilms.
Collapse
Affiliation(s)
- An-Sofie D'Hondt
- Department of Biology, Marine Biology Lab, Ghent University, 9000 Ghent, Belgium; Department of Biology, Protistology and Aquatic Ecology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Willem Stock
- Department of Biology, Protistology and Aquatic Ecology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Lander Blommaert
- Department of Biology, Protistology and Aquatic Ecology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Tom Moens
- Department of Biology, Marine Biology Lab, Ghent University, 9000 Ghent, Belgium
| | - Koen Sabbe
- Department of Biology, Protistology and Aquatic Ecology Research Group, Ghent University, 9000 Ghent, Belgium.
| |
Collapse
|
27
|
Wenzel MA, Douglas A, Piertney SB. Microbiome composition within a sympatric species complex of intertidal isopods (Jaera albifrons). PLoS One 2018; 13:e0202212. [PMID: 30157257 PMCID: PMC6114722 DOI: 10.1371/journal.pone.0202212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/29/2018] [Indexed: 02/05/2023] Open
Abstract
The increasingly recognised effects of microbiomes on the eco-evolutionary dynamics of their hosts are promoting a view of the "hologenome" as an integral host-symbiont evolutionary entity. For example, sex-ratio distorting reproductive parasites such as Wolbachia are well-studied pivotal drivers of invertebrate reproductive processes, and more recent work is highlighting novel effects of microbiome assemblages on host mating behaviour and developmental incompatibilities that underpin or reinforce reproductive isolation processes. However, examining the hologenome and its eco-evolutionary effects in natural populations is challenging because microbiome composition is considerably influenced by environmental factors. Here we illustrate these challenges in a sympatric species complex of intertidal isopods (Jaera albifrons spp.) with pervasive sex-ratio distortion and ecological and behavioural reproductive isolation mechanisms. We deep-sequence the bacterial 16S rRNA gene among males and females collected in spring and summer from two coasts in north-east Scotland, and examine microbiome composition with a particular focus on reproductive parasites. Microbiomes of all species were diverse (overall 3,317 unique sequences among 3.8 million reads) and comprised mainly Proteobacteria and Bacteroidetes taxa typical of the marine intertidal zone, in particular Vibrio spp. However, we found little evidence of the reproductive parasites Wolbachia, Rickettsia, Spiroplasma and Cardinium, suggesting alternative causes of sex-ratio distortion. Notwithstanding, a significant proportion of the variance in microbiome composition among samples was explained by sex (14.1 %), nested within geographic (26.9 %) and seasonal (39.6 %) variance components. The functional relevance of this sex signal was difficult to ascertain given the absence of reproductive parasites, the ephemeral nature of the species assemblages and substantial environmental variability. These results establish the Jaera albifrons species complex as an intriguing system for examining the effects of microbiomes on reproductive processes and speciation, and highlight the difficulties associated with snapshot assays of microbiome composition in dynamic and complex environments.
Collapse
Affiliation(s)
- Marius A. Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Alex Douglas
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Stuart B. Piertney
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| |
Collapse
|
28
|
Parfrey LW, Moreau CS, Russell JA. Introduction: The host-associated microbiome: Pattern, process and function. Mol Ecol 2018; 27:1749-1765. [DOI: 10.1111/mec.14706] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Laura Wegener Parfrey
- Department of Botany; Biodiversity Research Centre; University of British Columbia; Vancouver British Columbia Canada
- Department of Zoology; University of British Columbia; Vancouver British Columbia Canada
| | - Corrie S. Moreau
- Department of Science and Education; Field Museum of Natural History; Chicago IL USA
| | | |
Collapse
|