Marine Sponges as <italic toggle="yes">Chloroflexi</italic> Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade

ABSTRACT Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldiline...

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Autores principales:	Kristina Bayer, Martin T. Jahn, Beate M. Slaby, Lucas Moitinho-Silva, Ute Hentschel
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	Chloroflexi DOM degradation FISH-CLEM metabolism metagenomic binning single-cell genomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/58064d0b54e649a2a6576dd2cbeda2c3
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spelling	oai:doaj.org-article:58064d0b54e649a2a6576dd2cbeda2c32021-12-02T19:46:17ZMarine Sponges as <italic toggle="yes">Chloroflexi</italic> Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade10.1128/mSystems.00150-182379-5077https://doaj.org/article/58064d0b54e649a2a6576dd2cbeda2c32018-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00150-18https://doaj.org/toc/2379-5077ABSTRACT Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldilineae, and Anaerolineae being the most prominent. We performed metagenomic and single-cell genomic analyses to elucidate the functional gene repertoire of Chloroflexi symbionts of Aplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail. Common genomic features of Chloroflexi sponge symbionts were related to central energy and carbon converting pathways, amino acid and fatty acid metabolism, and respiration. Clade-specific metabolic features included a massively expanded genomic repertoire for carbohydrate degradation in Anaerolineae and Caldilineae genomes, but only amino acid utilization by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding components involved in cofactor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by the fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM) method. Carbohydrate degradation potential was reported previously for “Candidatus Poribacteria” and SAUL, typical symbionts of HMA sponges, and we propose here that HMA sponge symbionts collectively engage in degradation of dissolved organic matter, both labile and recalcitrant. Thus, sponge microbes may not only provide nutrients to the sponge host, but they may also contribute to dissolved organic matter (DOM) recycling and primary productivity in reef ecosystems via a pathway termed the sponge loop. IMPORTANCE Chloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought.Kristina BayerMartin T. JahnBeate M. SlabyLucas Moitinho-SilvaUte HentschelAmerican Society for MicrobiologyarticleChloroflexiDOM degradationFISH-CLEMmetabolismmetagenomic binningsingle-cell genomicsMicrobiologyQR1-502ENmSystems, Vol 3, Iss 6 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Chloroflexi DOM degradation FISH-CLEM metabolism metagenomic binning single-cell genomics Microbiology QR1-502
spellingShingle	Chloroflexi DOM degradation FISH-CLEM metabolism metagenomic binning single-cell genomics Microbiology QR1-502 Kristina Bayer Martin T. Jahn Beate M. Slaby Lucas Moitinho-Silva Ute Hentschel Marine Sponges as <italic toggle="yes">Chloroflexi</italic> Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade
description	ABSTRACT Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldilineae, and Anaerolineae being the most prominent. We performed metagenomic and single-cell genomic analyses to elucidate the functional gene repertoire of Chloroflexi symbionts of Aplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail. Common genomic features of Chloroflexi sponge symbionts were related to central energy and carbon converting pathways, amino acid and fatty acid metabolism, and respiration. Clade-specific metabolic features included a massively expanded genomic repertoire for carbohydrate degradation in Anaerolineae and Caldilineae genomes, but only amino acid utilization by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding components involved in cofactor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by the fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM) method. Carbohydrate degradation potential was reported previously for “Candidatus Poribacteria” and SAUL, typical symbionts of HMA sponges, and we propose here that HMA sponge symbionts collectively engage in degradation of dissolved organic matter, both labile and recalcitrant. Thus, sponge microbes may not only provide nutrients to the sponge host, but they may also contribute to dissolved organic matter (DOM) recycling and primary productivity in reef ecosystems via a pathway termed the sponge loop. IMPORTANCE Chloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought.
format	article
author	Kristina Bayer Martin T. Jahn Beate M. Slaby Lucas Moitinho-Silva Ute Hentschel
author_facet	Kristina Bayer Martin T. Jahn Beate M. Slaby Lucas Moitinho-Silva Ute Hentschel
author_sort	Kristina Bayer
title	Marine Sponges as <italic toggle="yes">Chloroflexi</italic> Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade
title_short	Marine Sponges as <italic toggle="yes">Chloroflexi</italic> Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade
title_full	Marine Sponges as <italic toggle="yes">Chloroflexi</italic> Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade
title_fullStr	Marine Sponges as <italic toggle="yes">Chloroflexi</italic> Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade
title_full_unstemmed	Marine Sponges as <italic toggle="yes">Chloroflexi</italic> Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade
title_sort	marine sponges as <italic toggle="yes">chloroflexi</italic> hot spots: genomic insights and high-resolution visualization of an abundant and diverse symbiotic clade
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/58064d0b54e649a2a6576dd2cbeda2c3
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Marine Sponges as <italic toggle="yes">Chloroflexi</italic> Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade

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