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Vadillo Gonzalez S, Vranken S, Coleman MA, Wernberg T, Steinberg PD, Marzinelli EM. Host genotype and microbiome associations in co-occurring clonal and non-clonal kelp, Ecklonia radiata. Mol Ecol 2023; 32:4584-4598. [PMID: 37332135 DOI: 10.1111/mec.17056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 04/21/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023]
Abstract
A fundamental question in holobiont biology is the extent to which microbiomes are determined by host characteristics regulated by their genotype. Studies on the interactions of host genotype and microbiomes are emerging but disentangling the role that host genotype has in shaping microbiomes remains challenging in natural settings. Host genotypes tend to be segregated in space and affected by different environments. Here we overcome this challenge by studying an unusual situation where host asexual (5 clonal lineages) and sexual genotypes (15 non-clonal lineages) of the same species co-occur under the same environment. This allowed us to partition the influence of morphological traits and genotype in shaping host-associated bacterial communities. Lamina-associated bacteria of co-occurring kelp sexual non-clonal (Ecklonia radiata) and asexual clonal (E. brevipes) morphs were compared to test whether host genotype influences microbiomes beyond morphology. Similarity of bacterial composition and predicted functions were evaluated among individuals within a single clonal genotype or among non-clonal genotypes of each morph. Higher similarity in bacterial composition and inferred functions were found among identical clones of E. brevipes compared to other clonal genotypes or unique non-clonal E. radiata genotypes. Additionally, bacterial diversity and composition differed significantly between the two morphs and were related with one morphological trait in E. brevipes (haptera). Thus, factors regulated by the host genotype (e.g. secondary metabolite production) likely drive differences in microbial communities between morphs. The strong association of genotype and microbiome found here highlights the importance of genetic relatedness of hosts in determining variability in their bacterial symbionts.
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Affiliation(s)
- Sebastian Vadillo Gonzalez
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
| | - Sofie Vranken
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
| | - Melinda A Coleman
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- New South Wales Fisheries, Department of Primary Industries, National Marine Science Centre, Coffs Harbour, New South Wales, Australia
| | - Thomas Wernberg
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- Institute of Marine Research, Floedevigen Research Station, His, Norway
| | - Peter D Steinberg
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ezequiel M Marzinelli
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
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Mazzio E, Barnes A, Badisa R, Fierros-Romero G, Williams H, Council S, Soliman K. Functional immune boosters; the herb or its dead microbiome? Antigenic TLR4 agonist MAMPs found in 65 medicinal roots and algae's. J Funct Foods 2023; 107:105687. [PMID: 37654434 PMCID: PMC10469438 DOI: 10.1016/j.jff.2023.105687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
Background Humans have been consuming medicinal plants (as herbs/ spices) to combat illness for centuries while ascribing beneficial effects predominantly to the plant/phytochemical constituents, without recognizing the power of obligatory resident microorganism' communities (MOCs) (live/dead bacteria, fungus, yeast, molds etc.) which remain after industrial microbial reduction methods. Very little is known about the taxonomic identity of residual antigenic microbial associated molecular patterns (MAMPs) debris in our botanical over the counter (OTC) products, which if present would be recognized as foreign (non-self) antigenic matter by host pattern recognition receptors (PRRs) provoking a host immune response; this the basis of vaccine adjuvants. As of today, only few research groups have removed the herbal MAMP biomass from herbs, all suggesting that immune activation may not be from the plant but rather its microbial biomass; a hypothesis we corroborate. Purpose The purpose of this work was to conduct a high through put screening (HTPS) of over 2500 natural plants, OTC botanical supplements and phytochemicals to elucidate those with pro-inflammatory; toll like receptor 4 (TLR4) activating properties in macrophages. Study Design The HTPS was conducted on RAW 264.7 cells vs. lipopolysaccharide (LPS) E. coli 0111:B4, testing iNOS / nitric oxide production ( NO 2 - ) as a perimeter endpoint. The data show not a single drug/chemical/ phytochemical and approximately 98 % of botanicals to be immune idle (not effective) with only 65 pro-inflammatory (hits) in a potency range of LPS. Method validation studies eliminated the possibility of false artifact or contamination, and results were cross verified through multiple vendors/ manufacturers/lot numbers by botanical species. Lead botanicals were evaluated for plant concentration of LPS, 1,3:1,6-β-glucan, 1,3:1,4-β-D-glucan and α-glucans; where the former paralleled strength in vitro. LPS was then removed from plants using high-capacity endotoxin poly lysine columns, where bioactivity of LPS null "plant" extracts were lost. The stability of E.Coli 0111:B4 in an acid stomach mimetic model was confirmed. Last, we conducted a reverse culture on aerobic plate counts (APCs) from select hits, with subsequent isolation of gram-negative bacteria (MacConkey agar). Cultures were 1) heat destroyed (retested/ confirming bioactivity) and 2) subject to taxonomical identification by genetic sequencing 18S, ITS1, 5.8 s, ITS2 28S, and 16S. Conclusion The data show significant gram negative MAMP biomass dominance in A) roots (e.g. echinacea, yucca, burdock, stinging nettle, sarsaparilla, hydrangea, poke, madder, calamus, rhaponticum, pleurisy, aconite etc.) and B) oceanic plants / algae's (e.g. bladderwrack, chlorella, spirulina, kelp, and "OTC Seamoss-blends" (irish moss, bladderwrack, burdock root etc), as well as other random herbs (eg. corn silk, cleavers, watercress, cardamom seed, tribulus, duckweed, puffball, hordeum and pollen). The results show a dominance of gram negative microbes (e.g. Klebsilla aerogenes, Pantoae agglomerans, Cronobacter sakazakii), fungus (Glomeracaea, Ascomycota, Irpex lacteus, Aureobasidium pullulans, Fibroporia albicans, Chlorociboria clavula, Aspergillus_sp JUC-2), with black walnut hull, echinacea and burdock root also containing gram positive microbial strains (Fontibacillus, Paenibacillus, Enterococcus gallinarum, Bromate-reducing bacterium B6 and various strains of Clostridium). Conclusion This work brings attention to the existence of a functional immune bioactive herbal microbiome, independent from the plant. There is need to further this avenue of research, which should be carried out with consideration as to both positive or negative consequences arising from daily consumption of botanicals highly laden with bioactive MAMPS.
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Affiliation(s)
- E. Mazzio
- Florida Agricultural and Mechanical University, College of Pharmacy and Pharmaceutical Sciences, Tallahassee, FL 32307, United States
| | - A. Barnes
- Florida Agricultural and Mechanical University, College of Pharmacy and Pharmaceutical Sciences, Tallahassee, FL 32307, United States
| | - R. Badisa
- Florida Agricultural and Mechanical University, College of Pharmacy and Pharmaceutical Sciences, Tallahassee, FL 32307, United States
| | - G. Fierros-Romero
- Florida Agricultural and Mechanical University, School of Environment, Tallahassee, FL 32307, United States
| | - H. Williams
- Florida Agricultural and Mechanical University, School of Environment, Tallahassee, FL 32307, United States
| | - S. Council
- John Gnabre Science Research Institute, Baltimore, MD 21224, United States
| | - K.F.A. Soliman
- Florida Agricultural and Mechanical University, College of Pharmacy and Pharmaceutical Sciences, Tallahassee, FL 32307, United States
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Mazzio E, Barnes A, Badisa R, Council S, Soliman KFA. Plants against cancer: the immune-boosting herbal microbiome: not of the plant, but in the plant. Basic concepts, introduction, and future resource for vaccine adjuvant discovery. Front Oncol 2023; 13:1180084. [PMID: 37588095 PMCID: PMC10426289 DOI: 10.3389/fonc.2023.1180084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/30/2023] [Indexed: 08/18/2023] Open
Abstract
The presence of microorganism communities (MOCs) comprised of bacteria, fungi, archaea, algae, protozoa, viruses, and the like, are ubiquitous in all living tissue, including plant and animal. MOCs play a significant role in establishing innate and acquired immunity, thereby influencing susceptibility and resistance to disease. This understanding has fostered substantial advancements in several fields such as agriculture, food science/safety, and the development of vaccines/adjuvants, which rely on administering inactivated-attenuated MOC pathogens. Historical evidence dating back to the 1800s, including reports by Drs Busch, Coley, and Fehleisen, suggested that acute febrile infection in response to "specific microbes" could trigger spontaneous tumor remission in humans. This discovery led to the purposeful administration of the same attenuated strains, known as "Coley's toxin," marking the onset of the first microbial (pathogen) associated molecular pattern (MAMPs or PAMPs)-based tumor immunotherapy, used clinically for over four decades. Today, these same MAMPS are consumed orally by billions of consumers around the globe, through "specific" mediums (immune boosting "herbal supplements") as carriers of highly concentrated MOCs accrued in roots, barks, hulls, sea algae, and seeds. The American Herbal Products Association (AHPA) mandates microbial reduction in botanical product processing but does not necessitate the removal of dead MAMP laden microbial debris, which we ingest. Moreover, while existing research has focused on the immune-modulating role of plant phytochemicals, the actual immune-boosting properties might instead reside solely in the plant's MOC MAMP laden biomass. This assertion is logical, considering that antigenic immune-provoking epitopes, not phytochemicals, are known to stimulate immune response. This review explores a neglected area of research regarding the immune-boosting effects of the herbal microbiome - a presence which is indirectly corroborated by various peripheral fields of study and poses a fundamental question: Given that food safety focuses on the elimination of harmful pathogens and crop science acknowledges the existence of plant microbiomes, what precisely are the immune effects of ingesting MAMPs of diverse structural composition and concentration, and where are these distributed in our botanicals? We will discuss the topic of concentrated edible MAMPs as acid and thermally stable motifs found in specific herbs and how these would activate cognate pattern recognition receptors (PPRs) in the upper gut-associated lymphoid tissue (GALT), including Peyer's patches and the lamina propria, to boost antibody titers, CD8+ and CD4+ T cells, NK activity, hematopoiesis, and facilitating M2 to M1 macrophage phenotype transition in a similar manner as vaccines. This new knowledge could pave the way for developing bioreactor-grown/heat-inactivated MOC therapies to boost human immunity against infections and improve tumor surveillance.
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Affiliation(s)
- Elizabeth Mazzio
- Divison of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A & M University, Tallahassee, FL, United States
| | - Andrew Barnes
- Divison of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A & M University, Tallahassee, FL, United States
| | - Ramesh Badisa
- Divison of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A & M University, Tallahassee, FL, United States
| | - Stevie Council
- John Gnabre Science Research Institute, Baltimore, MD, United States
| | - Karam F. A. Soliman
- Divison of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A & M University, Tallahassee, FL, United States
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Massé A, Detang J, Duval C, Duperron S, Woo AC, Domart-Coulon I. Bacterial Microbiota of Ostreobium, the Coral-Isolated Chlorophyte Ectosymbiont, at Contrasted Salinities. Microorganisms 2023; 11:1318. [PMID: 37317290 DOI: 10.3390/microorganisms11051318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Microscopic filaments of the siphonous green algae Ostreobium (Ulvophyceae, Bryopsidales) colonize and dissolve the calcium carbonate skeletons of coral colonies in reefs of contrasted salinities. Here, we analyzed their bacterial community's composition and plasticity in response to salinity. Multiple cultures of Pocillopora coral-isolated Ostreobium strains from two distinct rbcL lineages representative of IndoPacific environmental phylotypes were pre-acclimatized (>9 months) to three ecologically relevant reef salinities: 32.9, 35.1, and 40.2 psu. Bacterial phylotypes were visualized for the first time at filament scale by CARD-FISH in algal tissue sections, within siphons, at their surface or in their mucilage. Ostreobium-associated microbiota, characterized by bacterial 16S rDNA metabarcoding of cultured thalli and their corresponding supernatants, were structured by host genotype (Ostreobium strain lineage), with dominant Kiloniellaceae or Rhodospirillaceae (Alphaproteobacteria, Rhodospirillales) depending on Ostreobium lineage, and shifted Rhizobiales' abundances in response to the salinity increase. A small core microbiota composed of seven ASVs (~1.5% of thalli ASVs, 19-36% cumulated proportions) was persistent across three salinities in both genotypes, with putative intracellular Amoebophilaceae and Rickettsiales_AB1, as well as Hyphomonadaceae and Rhodospirillaceae also detected within environmental (Ostreobium-colonized) Pocillopora coral skeletons. This novel knowledge on the taxonomic diversity of Ostreobium bacteria paves the way to functional interaction studies within the coral holobiont.
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Affiliation(s)
- Anaïs Massé
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
| | - Juliette Detang
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
| | - Charlotte Duval
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
| | - Sébastien Duperron
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
| | - Anthony C Woo
- Pôle Analyse de Données UAR 2700 2AD, Muséum National d'Histoire Naturelle (MNHN), 43 Rue Cuvier, 75005 Paris, France
| | - Isabelle Domart-Coulon
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
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Osborne MG, Molano G, Simons AL, Dao V, Ong B, Vong B, Singh A, Montecinos Arismendi GJ, Alberto F, Nuzhdin SV. Natural variation of Macrocystis pyrifera gametophyte germplasm culture microbiomes and applications for improving yield in offshore farms. JOURNAL OF PHYCOLOGY 2023; 59:402-417. [PMID: 36727292 DOI: 10.1111/jpy.13320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 11/11/2022] [Accepted: 01/04/2023] [Indexed: 05/28/2023]
Abstract
With national interest in seaweed-based biofuels as a sustainable alternative to fossil fuels, there is a need for tools that produce high-yield seaweed cultivars and increase the efficiency of offshore farms. Several agricultural studies have demonstrated that the application of microbial inoculants at an early life stage can improve crop yield, and there is an opportunity to use similar techniques in seaweed aquaculture. However, there is a critical knowledge gap regarding host-microbiome associations of macroalgae gametophytes in germplasm cultures. Here, we investigate the microbial community of Macrocystis pyrifera gametophyte germplasm cultures that were used to cultivate an offshore farm in Santa Barbara, California and identify key taxa correlated with increased biomass of mature sporophytes. This work provides a valuable knowledge base for the development of microbial inoculants that produce high-biomass M. pyrifera cultivars to ultimately be used as biofuel feedstocks.
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Affiliation(s)
- Melisa G Osborne
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Gary Molano
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Ariel Levi Simons
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, USA
| | - Valerie Dao
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Brandon Ong
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Brandon Vong
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Anupam Singh
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | | | - Filipe Alberto
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Sergey V Nuzhdin
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
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Park J, Davis K, Lajoie G, Parfrey LW. Alternative approaches to identify core bacteria in Fucus distichus microbiome and assess their distribution and host-specificity. ENVIRONMENTAL MICROBIOME 2022; 17:55. [PMID: 36384808 PMCID: PMC9670562 DOI: 10.1186/s40793-022-00451-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Identifying meaningful ecological associations between host and components of the microbiome is challenging. This is especially true for hosts such as marine macroalgae where the taxonomic composition of the microbiome is highly diverse and variable in space and time. Identifying core taxa is one way forward but there are many methods and thresholds in use. This study leverages a large dataset of microbial communities associated with the widespread brown macroalga, Fucus distichus, across sites and years on one island in British Columbia, Canada. We compare three different methodological approaches to identify core taxa at the amplicon sequence variant (ASV) level from this dataset: (1) frequency analysis of taxa on F. distichus performed over the whole dataset, (2) indicator species analysis (IndVal) over the whole dataset that identifies frequent taxa that are enriched on F. distichus in comparison to the local environment, and (3) a two-step IndVal method that identifies taxa that are consistently enriched on F. distichus across sites and time points. We then investigated a F. distichus time-series dataset to see if those core taxa are seasonally consistent on another remote island in British Columbia, Canada. We then evaluate host-specificity of the identified F. distichus core ASVs using comparative data from 32 other macroalgal species sampled at one of the sites. RESULTS We show that a handful of core ASVs are consistently identified by both frequency analysis and IndVal approaches with alternative definitions, although no ASVs were always present on F. distichus and IndVal identified a diverse array of F. distichus indicator taxa across sites on Calvert Island in multiple years. Frequency analysis captured a broader suit of taxa, while IndVal was better at identifying host-specific microbes. Finally, two-step IndVal identified hundreds of indicator ASVs for particular sites/timepoints but only 12 that were indicators in a majority (> 6 out of 11) of sites/timepoints. Ten of these ASVs were also indicators on Quadra Island, 250 km away. Many F. distichus-core ASVs are generally found on multiple macroalgal species, while a few ASVs are highly specific to F. distichus. CONCLUSIONS Different methodological approaches with variable set thresholds influence core identification, but a handful of core taxa are apparently identifiable as they are widespread and temporally associated with F. distichus and enriched in comparison to the environment. Moreover, we show that many of these core ASVs of F. distichus are found on multiple macroalgal hosts, indicating that most occupy a macroalgal generalist niche rather than forming highly specialized associations with F. distichus. Further studies should test whether macroalgal generalists or specialists are more likely to engage in biologically important exchanges with host.
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Affiliation(s)
- Jungsoo Park
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
| | - Katherine Davis
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
| | - Geneviève Lajoie
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, QC Canada
| | - Laura Wegener Parfrey
- Department of Botany, Biodiversity Research Centre, University of British Columbia, Vancouver, BC Canada
- Department of Zoology, University of British Columbia, Vancouver, BC Canada
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Abstract
Coastal marine macrophytes exhibit some of the highest rates of primary productivity in the world. They have been found to host a diverse set of microbes, many of which may impact the biology of their hosts through metabolisms that are unique to microbial taxa. Here, we characterized the metabolic functions of macrophyte-associated microbial communities using metagenomes collected from 2 species of kelp (Laminaria setchellii and Nereocystis luetkeana) and 3 marine angiosperms (Phyllospadix scouleri, P. serrulatus, and Zostera marina), including the rhizomes of two surfgrass species (Phyllospadix spp.), the seagrass Zostera marina, and the sediments surrounding P. scouleri and Z. marina. Using metagenomic sequencing, we describe 63 metagenome-assembled genomes (MAGs) that potentially benefit from being associated with macrophytes and may contribute to macrophyte fitness through their metabolic activity. Host-associated metagenomes contained genes for the use of dissolved organic matter from hosts and vitamin (B1, B2, B7, B12) biosynthesis in addition to a range of nitrogen and sulfur metabolisms that recycle dissolved inorganic nutrients into forms more available to the host. The rhizosphere of surfgrass and seagrass contained genes for anaerobic microbial metabolisms, including nifH genes associated with nitrogen fixation, despite residing in a well-mixed and oxygenated environment. The range of oxygen environments engineered by macrophytes likely explains the diversity of both oxidizing and reducing microbial metabolisms and contributes to the functional capabilities of microbes and their influences on carbon and nitrogen cycling in nearshore ecosystems. IMPORTANCE Kelps, seagrasses, and surfgrasses are ecosystem engineers on rocky shorelines, where they show remarkably high levels of primary production. Through analysis of their associated microbial communities, we found a variety of microbial metabolisms that may benefit the host, including nitrogen metabolisms, sulfur oxidation, and the production of B vitamins. In turn, these microbes have the genetic capabilities to assimilate the dissolved organic compounds released by their macrophyte hosts. We describe a range of oxygen environments associated with surfgrass, including low-oxygen microhabitats in their rhizomes that host genes for nitrogen fixation. The tremendous productivity of coastal seaweeds and seagrasses is likely due in part to the activities of associated microbes, and an increased understanding of these associations is needed.
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Weigel BL, Miranda KK, Fogarty EC, Watson AR, Pfister CA. Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes. mSystems 2022; 7:e0142221. [PMID: 35642511 PMCID: PMC9238374 DOI: 10.1128/msystems.01422-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/13/2022] [Indexed: 11/20/2022] Open
Abstract
Eukaryotic organisms evolved in a microbial world and often have intimate associations with diverse bacterial groups. Kelp, brown macroalgae in the order Laminariales, play a vital role in coastal ecosystems, yet we know little about the functional role of the microbial symbionts that cover their photosynthetic surfaces. Here, we reconstructed 79 bacterial metagenome-assembled genomes (MAGs) from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine their metabolic potential and functional roles. Despite the annual life history of bull kelp, nearly half of the bacterial MAGs were detected across multiple years. Diverse members of the kelp microbiome, spanning 6 bacterial phyla, contained genes for transporting and assimilating dissolved organic matter (DOM), which is secreted by kelp in large quantities and likely fuels the metabolism of these heterotrophic bacteria. Bacterial genomes also contained alginate lyase and biosynthesis genes, involved in polysaccharide degradation and biofilm formation, respectively. Kelp-associated bacterial genomes contained genes for dissimilatory nitrate reduction and urea hydrolysis, likely providing a reduced source of nitrogen to the host kelp. The genome of the most abundant member of the kelp microbiome and common macroalgal symbiont, Granulosicoccus, contained a full suite of genes for synthesizing cobalamin (vitamin B12), suggesting that kelp-associated bacteria have the potential to provide their host kelp with vitamins. Finally, kelp-associated Granulosicoccus contained genes that typify the aerobic anoxygenic phototrophic bacteria, including genes for bacteriochlorophyll synthesis and photosystem II reaction center proteins, making them the first known photoheterotrophic representatives of this genus. IMPORTANCE Kelp (brown algae in the order Laminariales) are foundational species that create essential habitat in temperate and arctic coastal marine ecosystems. These photosynthetic giants host millions of microbial taxa whose functions are relatively unknown, despite their potential importance for host-microbe interactions and nutrient cycling in kelp forest ecosystems. We reconstructed bacterial genomes from metagenomic samples collected from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine the functional gene content of specific members of the kelp microbiome. These bacterial genomes spanned 6 phyla and 19 families and included common alga-associated microbial symbionts such as Granulosicoccus. Key functions encoded in kelp-associated bacterial genomes included dissolved organic matter assimilation, alginate metabolism, vitamin B12 biosynthesis, and nitrogen reduction from nitrate and urea to ammonium, potentially providing the host kelp with vitamins and reduced nitrogen.
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Affiliation(s)
- Brooke L. Weigel
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA
| | | | - Emily C. Fogarty
- Committee on Microbiology, University of Chicago, Chicago, Illinois, USA
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Andrea R. Watson
- Committee on Microbiology, University of Chicago, Chicago, Illinois, USA
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Catherine A. Pfister
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, USA
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Wood G, Steinberg PD, Campbell AH, Vergés A, Coleman MA, Marzinelli EM. Host genetics, phenotype and geography structure the microbiome of a foundational seaweed. Mol Ecol 2022; 31:2189-2206. [PMID: 35104026 PMCID: PMC9540321 DOI: 10.1111/mec.16378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/18/2022] [Indexed: 12/01/2022]
Abstract
Interactions between hosts and their microbiota are vital to the functioning and resilience of macro-organisms. Critically, for hosts that play foundational roles in communities, understanding what drives host-microbiota interactions is essential for informing ecosystem restoration and conservation. We investigated the relative influence of host traits and the surrounding environment on microbial communities associated with the foundational seaweed Phyllospora comosa. We quantified 16 morphological and functional phenotypic traits, including host genetics (using 354 single nucleotide polymorphisms) and surface-associated microbial communities (using 16S rRNA gene amplicon sequencing) from 160 individuals sampled from eight sites spanning Phyllospora's entire latitudinal distribution (1,300 km). Combined, these factors explained 54% of the overall variation in Phyllospora's associated microbial community structure, much of which was related to the local environment (~32%). We found that putative "core" microbial taxa (i.e., present on all Phyllospora individuals sampled) exhibited slightly higher associations with host traits when compared to "variable" taxa (not present on all individuals). We identified several key genetic loci and phenotypic traits in Phyllospora that were strongly related to multiple microbial amplicon sequence variants, including taxa with known associations to seaweed defence, disease and tissue degradation. This information on how host-associated microbial communities vary with host traits and the environment enhances our current understanding of how "holobionts" (hosts plus their microbiota) are structured. Such understanding can be used to inform management strategies of these important and vulnerable habitats.
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Affiliation(s)
- Georgina Wood
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Peter D. Steinberg
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
- Sydney Institute of Marine ScienceSydneyNew South WalesAustralia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
| | - Alexandra H. Campbell
- USC Seaweed Research GroupUniversity of the Sunshine CoastSunshine CoastQueenslandAustralia
| | - Adriana Vergés
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Melinda A. Coleman
- Department of Primary IndustriesNational Marine Science CentreCoffs HarbourNew South WalesAustralia
| | - Ezequiel M. Marzinelli
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Sydney Institute of Marine ScienceSydneyNew South WalesAustralia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
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10
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Jin X, Yang Y, Cao H, Gao B, Zhao Z. Eco-phylogenetic analyses reveal divergent evolution of vitamin B 12 metabolism in the marine bacterial family 'Psychromonadaceae'. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:147-163. [PMID: 34921716 DOI: 10.1111/1758-2229.13036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Cobalamin (vitamin B12 ) is an essential micronutrient required by both prokaryotes and eukaryotes. Nevertheless, with high genetic and metabolic cost, de novo cobalamin biosynthesis is exclusive to a subset of prokaryotic taxa. Many Cyanobacterial and Archaeal taxa have been implicated in de novo cobalamin biosynthesis in epi- and mesopelagic ocean respectively. However, the contributions of Gammaproteobacteria particularly the family 'Psychromonadaceae' is largely unknown. Through phylo-pangenomic analyses using concatenated single-copy proteins and homologous gene clusters respectively, the phylogenies within 'Psychromonadaceae' recapitulate both their taxonomic delineations and environmental distributions. Moreover, uneven distribution of cobalamin de novo biosynthetic operon and cobalamin-dependent light-responsive regulon were observed, and of which the linkages to the environmental conditions where cobalamin availability and light regime can be varied respectively were discussed, suggesting the impacts of ecological divergence in shaping their disparate cobalamin-related metabolisms. Functional analysis demonstrated a varying degree of cobalamin dependency for both central metabolic processes and cobalamin-mediated light-responsive regulation, and underlying sequence characteristics of cis- and trans-regulatory elements were revealed. Our findings emphasized the potential roles of cobalamin in shaping the ecological distributions and driving the metabolic evolution in the marine bacterial family 'Psychromonadaceae', and have further implications for an improved understanding of nutritional interdependencies and community metabolism modulated by cobalamin.
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Affiliation(s)
- Xingkun Jin
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yaofang Yang
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Haihang Cao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Zhe Zhao
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
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11
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Davis KM, Mazel F, Parfrey LW. The microbiota of intertidal macroalgae Fucus distichus is site-specific and resistant to change following transplant. Environ Microbiol 2021; 23:2617-2631. [PMID: 33817918 DOI: 10.1111/1462-2920.15496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023]
Abstract
It is unclear how host-associated microbial communities will be affected by future environmental change. Characterizing how microbiota differ across sites with varying environmental conditions and assessing the stability of the microbiota in response to abiotic variation are critical steps towards predicting outcomes of environmental change. Intertidal organisms are valuable study systems because they experience extreme variation in environmental conditions on tractable timescales such as tide cycles and across small spatial gradients in the intertidal zone. Here we show a widespread intertidal macroalgae, Fucus distichus, hosts site-specific microbiota over small (meters to kilometres) spatial scales. We demonstrate stability of site-specific microbial associations by manipulating the host environment and microbial species pool with common garden and reciprocal transplant experiments. We hypothesized that F. distichus microbiota would readily shift to reflect the contemporary environment due to selective filtering by abiotic conditions and/or colonization by microbes from the new environment or nearby hosts. Instead, F. distichus microbiota was stable for days after transplantation in both the laboratory and field. Our findings expand the current understanding of microbiota dynamics on an intertidal foundation species. These results may also point to adaptations for withstanding short-term environmental variation, in hosts and/or microbes, facilitating stable host-microbial associations.
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Affiliation(s)
- Katherine M Davis
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Hakai Institute, PO Box 309, Heriot Bay, BC, V0P 1H0, Canada
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